Based on a new trade accounting method-the trade in value-added accounting method-this paper constructs the international manufacturing trade in value-added networks and preferential trade agreement (PTA) networks and uses the complex network analysis method to explore the relations between PTA and international manufacturing trade in value-added from the perspective of the global value chain. The results are as follows: (1) Over the years, the international manufacturing trade in value-added networks and PTA networks has shown a significant clustering effect, and the size of networks has grown rapidly. (2) The TEX, DVA and FVA networks of the international manufacturing value added trade over the years can be divided into two societies in the Asia-Pacific region and the European region. This division just reflects the different modes of division of labor in the manufacturing value chain of the two major economic regions in the world. (3) QAP analysis shows that the influencing factors of the traditional gravity model can still explain the manufacturing trade network and its value-added trade network, while the influence of economic globalization, the enlargement of the EU and the internationalization strategy of enterprises, the PTA network and manufacturing value-added the relationship between trade networks changed from positive to negative in 2004.