Shigeru Iwasaki, who was chief of staff of the Japanese Self Defense Forces Joint Staff from 2012 to 2014, was named as an advisor to Taiwan's government in March, according to Taiwanese media.
The sanctions come as China and Japan are enmeshed in a row over prime minister Sanae Takaichi's suggestion in November that Tokyo could intervene militarily in any attack on the self-ruled democratic island.
China claims Taiwan as part of its territory and has threatened to use force to bring it under its control.
Beijing said on Monday that it firmly opposed Iwasaki taking up the advisor role.
The retired general has "openly colluded with 'Taiwan independence' separatist forces, seriously violating the one-China principle... and damaging China's sovereignty and territorial integrity", the foreign ministry said in a statement.
Under the announced "countermeasures", the 72-year-old is banned from entering China, including Hong Kong and Macau, and any assets he has in the country will be frozen.
People and organisations in China are also barred from working with him, the ministry said.
Japan's foreign ministry said that it was "regrettable for the Chinese side to take a unilateral measure that seems to intimidate someone with a different position".
Taiwan, which rejects China's claims on its territory, also hit back.
"China has no jurisdiction over the participation of the Taiwanese people or citizens of other countries in political, public or democratic activities in Taiwan or in third countries," Taipei's foreign ministry said.
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