Constrained by export costs, some small and medium-sized enterprises and inefficient enterprises will choose to export products indirectly through trade intermediaries. The trade facilitation of countries in the world has effectively reduced the transaction cost of international trade, prompting some indirect export enterprises to switch to direct export, and the sustainable development of trade intermediaries has been challenged. However, the existing literature seldom studies the economic effects of trade facilitation from the perspective of trade intermediaries, especially the lack of empirical analysis of its heterogeneity. This paper holds that the reform of destination trade facilitation will reduce the threshold for foreign enterprises to export products, weaken the role of trade intermediary in export trade, and reduce indirect export products of exporting countries; since the economic effect of institutional changes usually shows a decreasing trend, for destinations and export products with a high proportion of indirect exports (relative inconvenience in trade), destination trade facilitation weakens the role of trade intermediary more significantly. Based on the Global Competitiveness Report and China Customs Data, this paper analyzes about 4 700 products exported by China to nearly 150 destinations from 2007 to 2015. The analysis shows that the improvement of the level of destination trade facilitation has significantly reduced the proportion of China’s indirect exports in the export value (volume) of its products, resulting in a decline in the intermediary role of China’s product exports. This paper further sets up several dummy variables of destination types and export product types, and tests the heterogeneity of the effect of destination trade facilitation on the intermediary effect of export trade through the moderating effect model. The results show that, relatively speaking, for the sample destinations that are inconvenient to trade, have low incomes, have low levels of development, and have not signed FTA with China, and do not belong to the “Belt and Road” region, the increase in the level of trade facilitation has a greater negative impact on the proportion (volume) of indirect exports of Chinese products, and the proportion (volume) of indirect exports of necessities, products with low technical complexity, and products of special trade concern declined more significantly when the level of trade facilitation at the destination increased. Compared with the existing literature, this paper mainly expands and deepens the research in the following two aspects: on one hand, this paper explores the weakening effect of destination trade facilitation on the intermediary effect of export trade and its destination heterogeneity and export product heterogeneity, and expands the research perspective on the economic effect of trade facilitation; on the other hand, taking China’s export products as a research sample, this paper provides empirical evidence for the effect of destination trade facilitation on trade intermediation and its heterogeneity, and helps to deepen our understanding of the intermediary role of export trade. The research in this paper reveals the weakening effect of destination trade facilitation on the intermediary effect of export trade and its heterogeneity in destination types and export product types, which can provide path guidance and strategic inspiration for the transformation and upgrading and high-quality development of trade intermediaries in the new development stage, thereby promoting trade intermediaries to play a more active role in building a new development pattern.