The ban, effective Thursday, applies to officials with access to classified information, as well as ministers, mayors and country magistrates.
BBC's Cindy Sui in Taipei says there are concerns that they may inadvertently reveal information.
It comes as relations between the two sides are already strained.
Some officials choose China for further education partly because they want to build connections to generate trade and investment opportunities.
But there have also been a string of cases involving Taiwanese defence ministry officials spying for China, our correspondent says.
"The ministry has discussed the matter for some time and published the revised regulations in view of national security," said Interior Minister Chen Wei-zen on Wednesday.
State media Focus Taiwan cited National Security Bureau data that showed 97 civil servants went to China between 2004 and 2013, mainly to pursue doctorates.
They mainly studied at Xiamen University in Fujian Prince, China University of Political Science and Law in Beijing and Jinan University in Guangzhou, Focus Taiwan said.
Relations between the two sides were frayed earlier this year when protests broke out in Taiwan over a trade deal with China. In March, student protesters occupied the parliament building.
In October, Taiwan's President Ma Ying-jeou voiced support for Hong Kong's pro-democracy movement, angering Chinese officials.
There are also increasing worries about China's growing influence in Taiwan, our correspondent reports.
Beijing claims Taiwan as a province of China with hopes of reunification at some point.
創作內容
Taiwan bans senior officials from studying in China
天南地北 (5)