The English Civil War was part of an ongoing conflict within the English political system with regard to how much power the monarch and Parliament should have respectively.
The civil war began when King James I became king of England after the death of Queen Elizabeth I. James was the king of Scotland, where he was used to ruling in a fairly absolute way. He believed in the divine right of kings.
In England, however, Parliament had a great deal of power. Parliament did not want to allow the king to take the power that they felt was theirs. This was the fundamental cause of the civil war.
There was also a religious aspect to the war. James supported the Anglican Church the way it was at that time. He liked the hierarchical nature of the church because he saw it as a support for the monarchy. However, much of Parliament and England was Puritan. They disliked the hierarchical nature of the Church of England, seeing it as too much like the Catholic Church.
These related issues caused the war. It was a war over the relative amounts of power that the king and Parliament should have.