Peng Ming, who has been incarcerated since 2005 in Hubei Province, was serving a life sentence for publically advocating democratic reform.
The Communist Party has taken a hard line on Christianity since Chairman Mao came to power in 1949.
Mao threw more than 10,000 missionaries out of China at the start of his reign.
The party seized church property and killed or imprisoned Chinese Christians.
Now, Christians have the right to worship at join state-controlled churches.
Many choose to worship in house churches instead. Christians still face prejudice and even imprisonment for their beliefs.
In 1998 Ming had set up the organisation the China New Development Strategy Research Institute, where he led weekly discussions on democracy.
He was arrested multiple times before fleeing to Thailand and then the US.
In May 2004 Ming was illegally transported to China where he was arrested and sentenced to life imprisonment in 2005.
The circumstances of Ming's death remain unclear, with the death certificate giving no details of the cause of death.
According to the news and commentary website China Change, many in the dissident community have "expressed doubt over the official version of events, particularly given the fact that Peng's older brother visited him as recently as November 24, and reported that he appeared to be in good health".
Christian Solidarity Worldwide's Chief Executive Mervyn Thomas said: "Peng Ming's death, after more than ten years detention and separation from his family in the US, is a tragedy.
"We urge the authorities to make clear the reasons for his death, and to investigate any possibility of ill-treatment."