Pastor Li Juncai was charged with "disrupting public service" after he challenged the arrival of police-escorted demolition crews at Zhongxin Church in the Henan province.
The house church has a congregation of 700 members and was targeted as part of the government crackdown on unofficial churches.
Eyewitnesses said around ten Christians - mainly women and elderly people - were beaten and taken away when they attempted to block the access of two cranes, Christian charity Barnabas Fund reported.
One of the witnesses said: "Police took away congregants...and beat those who resisted. Also, some Christians were dragged away."
Once the cross was removed, the demolition team installed a flagpole to display China's national flag.
More than 4,000 crosses have reportedly been removed from churches in Henan since the middle of last year.
Chines authorities have increased their level of harassment against churches in the country since the Christmas period.
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