Napoleon did not really reform the Church itself. Instead, he worked to reform the relationship between the Catholic Church and French society.
The Catholic Church had been a major opponent of the French Revolution. When Napoleon came to power, he essentially made peace with the Church. He signed a "Concordat" with the pope that reformed the relationship between the Church and France. In the Concordat, Napoleon allowed the Church to reorganize in France. The Church was allowed once again to operate in the country. However, Napoleon did not restore it to its previous (pre-Revolution) status as the official religion of France. Instead, it became just one of the religions, albeit that of the majority of the people. Napoleon also refused to force the return to the Church of lands that had been confiscated.
In this way, Napoleon backed away from the truly anti-Church policies of the Revolution, but did not allow the Church to regain the power it had once had.