Chinese equities were worth $6.09 trillion compared with $6.17 trillion in Japan, according to data compiled by Bloomberg.
China took the number-two spot from Japan in 2014, then soared to an all-time high of more than $10 trillion in 2015.
The US has the world’s largest stock market at over $31 trillion, Presstv reported.
World economy suffers under Trump
The threat of a trade war with the United States has been cited as the cause of China's slower economic growth.
US pressure on China increased this week when the White House said it was considering more tariffs on a range of Chinese imports worth $200 billion.
The Trump administration has already imposed tariffs on $34 billion of Chinese goods last month and is considering another $16 billion in the coming days or weeks. This, prompted immediate retaliation from China
"Losing the ranking to Japan is the damage caused by the trade war," Banny Lam, head of research at CEB International Investment in Hong Kong, told Bloomberg News.
"Investors are paying attention to government policies as the US-China trade war will remain uncertain for now," Yoshihiro Okumura, general manager at Chibagin Asset Management, said in Tokyo.
"On the other hand, Japanese companies are showing strong results in general, sustaining share prices on the Tokyo Stock Exchange."
Okumura noted,however, that the global trade war launched by the US under Trump would have a negative impact on all countries economies.
"The Tokyo market is not in top form. The country is also subject to the trade war as it is heavily relying on global trade."