In this paper, we study the realistic influence of Chinese manufacturing enterprises’embedding in the global value chain on enterprises’markup and the influencing mechanism. The study results show that: in general, the deeper degree of global value chain embedment will significantly inhibit the increase of the cost markup of manufacturing, but it is found by subsample test that the deeper degree of global value chain embedment has more negative impact on markup of domestic enterprises than that of foreign enterprises, has significant positive effect on general trading enterprises and significant negative effect on processing enterprises, has significant positive effect on high-tech enterprises and significant negative effect on medium and low technology enterprises. In addition, the productivity, labor factor price and intermediate product factor price are the important intermediary factors that affect the markup of enterprises. The reality that global value chain embedding affects the export markup should be objectively recognized, especially under the influence of the current Sino-US trade friction, COVID-19 epidemic, the Russia-Ukraine conflict and other events, there is a great risk of fluctuation in the depth of China’s manufacturing global value chain embeddedness, and the increase of the manufacturing export markup should not be taken too hastily.