In short, Sir Syed made four main contributions to religious thought. First, he removed the western misunderstandings about Islam, second, he advocated Islam was a true religion, based on reason and natural laws, third, he washed off the accumulated dust of the centuries from the body of Islamic practices, and the fourth, he offered some fresh interpretations on a few Islamic beliefs in the new light of the age. He was supremely successful in the first three of his efforts, but on the fourth the Muslims had their own reservations. He thought of reconciling religion with science on the basis that science was truth, and religion was also truth, but people thought otherwise. Science is matter, religion is spirit.
Science is relative, religion is absolute.
Science is knowledge and religion is faith. Science is the intelligent understanding of the world, and religion is the intuitive contemplation of the universe. Science functions in time and space, religion penetrates time and space. Sir Syed did not make these distinctions. He thought science entered the domain of Divinity to explain the laws of nature which are nothing but the manifestation of Divine Will.