At the beginning of his work in the Bureau, he held a view to minimize the influence of religion in the socialist China.
There, he worked to prevent religious unrest, select the 11th Panchen Lama, and ban the controversial Falun Gong group.
In 1998, the Bureau of Religious Affairs was renamed the State Administration for Religious Affairs, while Ye Xiaowen remained its director.
He acknowledged presiding over religions in China, and changed policy to say that religion has a place in society, although he persecuted groups that he thought brought foreign control to Chinese churches, like the Roman Catholic Church.
In 2007 he declared State Religious Affairs Bureau Order No.
5, which attempted to reduce the influence of the 14th Dalai Lama and other foreign groups on the reincarnations in Tibet.
All the while, he traveled often to the United States to defend his religious policy against criticism.
Ye was relieved of his religious post in September 2009 to direct the Central Institute of Socialism.