When Charles raised his Standard in Nottingham 1642 it was unclear who, or how, the war would be won, but Parliament's Victory in The Civil War 1646, can be explained by a Multitude of reasons, most notably; a Royalist lack of finance [or more generally resources], and Parliamentary revolutionary Reform and Organisation.
Firstly the areas that Parliament held over the course of the civil war were more populous, wealthy and fertile than that of the Royalist's. Crucially Parliaments hold over London gave them significant privileges, including drawing funds from excise duties and a large, easily taxed, mercantile class. Whereas Royalist control lay over the poor, sparsely populated areas of the Country including Wales, the North, and portions of the Southwest.
Although in the first months of the war the Royalists were mostly better funded, despite their limited land held. This was due to Charles's support base, 75% of the English Aristocracy, who funded the initial stages of the war effort by selling their own possessions and raising personal regiments of Troop and Horse; also Parliaments main means of finance was taxation which took time to collect.
Parliament's acknowledgement for a need for organization of the war gave Parliament another advantage over the Royalists. An example of this is The Committee of Safety, first established on 4 July 1642, its purpose was liaise between the Members of Parliament at Westminster and Parliament's armies in the field. However disagreements over strategy reduced the Committee's effectiveness and Parliament achieved limited military success under its direction. Though the Royalists had far more organization problems, the King only first called the Oxford Parliament in December 1643.
Parliament took a decisive step by securing the alliance of the Presbyterian Scots in accepting the Solemn League and Covenant. A Scottish army, under Alexander Leslie, advanced into Yorkshire early in 1644 and gave aid to the parliamentary army in the north. This led to the battle of Marston Moor (July 2, 1644), in which Cromwell, leading Parliament, and Leslie inflicted a crushing defeat on the royalists. The Royalists had lost their Northern foothold, the city of York. This further exacerbated the Royalists already inferior resources reducing potential recruitment grounds and a valuable place to tax.
The radical reform such as the Self Denying Ordinance 1645 proved advantageous to the Parliamentary cause. It was clear that Essex and Manchester were at best halfhearted in pursuing the fight against the royalists In response to this the Self Denying Ordinance was prepared, and after a secondary redraft, the bill outlined that required resignations from all members of both House's, but did not forbid reappointment of the officers. The Self-denying ordinance improved military unity by separating the quarrels in Parliament from the immediate operations of command. In practical terms, the Ordinance solidified the power of Cromwell and his "war party" faction. A comparison of Commanders to provide an analysis of why Parliament won is required. In the Initial stages of the war the two most senior Parliamentarian commanders were the Earl of Essex and the Earl of Manchester, chosen because of their prestige rather than military abilities, characteristically reluctant to deliver a decisive blow to the Royalist cause and seemingly seeking for peace rather than a victory.
Whereas the Royalist's were led by the young, flamboyant and enthusiastic Prince Rupert, Charles's nephew, an experienced fighter on the continent and renowned for his triumphant cavalry charges, as seen at Edge Hill 1642, though also shown at Edge Hill was Rupert's inability to instil discipline in his cavalry which arguably resulted in the miss of a potential great victory. However in the latter stages of the war new commanders replaced the Parliamentarians command, based on Merit rather than Title. These were Sir Thomas Fairfax and his Lieutenant Oliver Cromwell.
Cromwell was careful to recruit only "godly, honest men" as his troopers and to lead them with firm discipline. Sir Thomas Fairfax was a gallant and courageous commander who led the New Model Army to a decisive Victory at the Battle of Naseby 1645.
The New Model Army was a remodelling of the Parliamentarian Army, first proposed by Sir William Waller 1644, which had a significant contribution to Parliaments victory. The changes included, officers that were appointed and promoted on merit rather than on their status, regular pay of eight pence a day, in exchange for guaranteed regular pay there was a ban on the looting and plundering of occupied towns and baggage trains and with it a new emphasis on discipline. Within months of its formation, the New Model inflicted a decisive defeat on the Royalists at the battle of Naseby, and brought the First Civil War to an end the following year.