In the past 30 years, with the reform and opening up of China's mainland, the increasingly close trade with Taiwan, there has been a steady development across the Taiwan Straits. But in recent years, the emergence of political parties in Taiwan has broken this balance. Based on the analysis and comparison of the existing literature, this paper focuses on the factors affecting the trade relationship between the two sides of the Taiwan Straits based on the comparison of the trade structure between China and Taiwan. It is the political factor that sums up the greatest impact on cross-strait trade relations. Finally, it predicts the development prospects of trade relations between the two sides of the strait, and proposes government assistance, preferential Taiwan, new areas of exploration, and promotion of direct investment to promote trade cooperation between the two sides of the strait.