Ma, who belongs to the Beijing-friendly main opposition party Kuomintang, was president of the democratic island from 2008 to 2016.
He oversaw warmer relations between Taiwan and China which culminated in a 2015 summit between him and Chinese President Xi Jinping -- a rare meeting of Beijing and Taipei's leaders.
Tensions soared after Ma's successor Tsai Ing-wen of the Democratic Progressive Party (DPP) took office in 2016 and rejected China's claim of sovereignty over the self-ruled island.
Ma, who is leading a student delegation for the trip, said exchanges between young people in China and Taiwan were important when "cross-strait relations are far more tense than when we were in power."
He said he hoped such contact would help to "build a bridge for peace across political danger".
"I often say that there will be fewer conflicts between the two sides in the future with more cross-strait youth exchanges and deeper understanding between them," Ma told reporters at Taipei's international airport before his flight to Shanghai.
The group will visit the northeastern city of Harbin and the southwestern city of Chengdu, Hsiao Hsu-tsen from the Ma Ying-jeou Foundation said previously.
It is not clear if Ma will meet with Xi during this trip. The two men reportedly met in Beijing in April for the first time since the 2015 summit.
Ma's trip follows a rare visit to Taiwan by Chinese politicians from Shanghai this week for an annual forum hosted this year by the Kuomintang-led Taipei City government.
Beijing severed high-level communications with Taipei after Tsai took office in 2016 and ramped up military pressure, with regular deployments of fighter jets and warships around the island.
Taipei said last week that Beijing had held its biggest maritime drills in years, stretching from near the southern islands of Japan to the South China Sea.
On Thursday, Taiwan said it had detected 16 Chinese warships in waters around the island, one of the highest numbers this year. That was a day after Taipei reported 53 Chinese military aircraft near the island, the most in a 24-hour window since a record 153 on October 15.
Relations between China and Taiwan have remained tense since Lai Ching-te, also from the DPP, succeeded Tsai in May.
Lai has been more outspoken than Tsai in defending Taiwan's sovereignty, angering Beijing, which calls him a "separatist".
Taiwanese officials said China last week held its biggest maritime drills in years, with around 90 ships deployed from near the southern islands of Japan to the South China Sea.
Beijing did not confirm the drills.
China and Taiwan have been ruled separately since 1949 when Chiang Kai-shek's nationalist forces were defeated by Mao Zedong's communist fighters and fled to the island.
While Taiwan considers itself a sovereign nation, China insists the island is part of its territory and has said it will not rule out using force to bring it under its control.
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