This paper proposes a value-added trade measurement model after a specific analysis of the extent of China and Japan’s participation in GVCs, the mode of participation and the status of division of labor, and the characteristics of the participation structure. Combined with the ratio of value-added to total exports, China is compared with major trading countries to study China’s level of value-added in GVCs, trade characteristics, and the proportion of China’s industry-wide development. Combined with the WIOD data, based on the model proposed in this paper, the bilateral trade interests of China and Japan, the bilateral export value, and the trade interest rate of both sides are measured from 2000 to 2014. The classification method of HS commodity code is used to extract the trade data of important time nodes between China and Japan and analyze the development of the structure of commodity trade between China and Japan. It measured that in 2014, the trade interest rate of China to Japan was 81.95%, and the export of 172.911 billion dollars contained 141.707 billion dollars of trade interest. Japan’s trade benefit rate to China was 73.94%, with $95.615 billion of trade benefits included in $129.314 billion of exports. It shows that as of 2014, China has replaced Japan in the bilateral trade between China and Japan to occupy a relatively favorable position, indicating that the international division of labor between China and Japan has gradually shifted from a vertical division of labor to a horizontal division of labor.