The incident at Longgang Huai En Church in the city of Wenzhou happened early on Monday morning and is part of a continuing crackdown on Christianity.
The country is seeing a boom in the number of people turning to the faith.
It's reported police used a crane to remove the cross whilst around 200 people peacefully protested against the move.
Officials claim it violated planning rules because it was too high – the same reason that has seen around 130 churches threatened with demolition.
Church leaders claim the country is discriminating against the growing Christian community.