Bush said in a statement that his visit to Kuanjie Church had shown "that God is universal, God is love and no state, no man, or woman should fear the influence of loving religion".
According to Dennis Wilder, a White House National Security official, President Bush pressed the case of religious freedom later in a meeting with Chinese President Hu Jintao.
"President Hu seemed to indicate that the door is open to religious freedom in China and that in the future there will be more room for religious believers," Wilder told reporters.
Bush is in China on an official visit that has so far struck a careful balance between diplomacy and fun at the Olympics, which opened in Beijing last Friday.
There were some media reports that Chinese activist Hua Huiqi had been arrested by police whilst on his way to the Kuanjie Church on Sunday, where Bush was taking part in a service.
According to China Aid Association, the movements of Hua, who was baptised at Kuanjie Church before joining unregistered house churches, had come under police surveillance in the months running up to the Olympics. Hua allegedly managed to escape from the police and remains on the run.
White House spokesman Gordon Johndroe told reporters, "While I can't confirm this specific report, we're disappointed anytime that someone is unable to worship freely."
Christians in China are split between official Three Self Patriotic Movement churches and unregistered house churches, which although theologically independent are the frequent targets of government repression.
Persecution watchdogs Open Doors and Release International have appealed to Christians around the world to pray for members of the house church movement over the period of the Olympics.