Bacillus thuringiensis (Bt) transgenic cotton is the unique Bt transgenic crop planted on a large scale in China, and its commercialized varieties and hectareage had increased rapidly in China during the past decade (1997-2006) with broad geographic distribution for the economic, environmental, and health benefits. In 2004, the planting area of Bt transgenic cotton in China ranked first worldwide with up to 370 × 106hm2. In addition, Bt transgenic rice varieties in field tests have been close to approval for commercialization. However, ecological risks, a complex issue of Bt transgenic crops on soil ecosystem is urgently faced in China due to more than 60 varieties transferred single or bivalent Bt genes grown under diverse geographic regions. Two main pathways, biomass incorporation and root exudates, are involved in the effects of Bt transgenic crops on soil ecosystems. In this paper, the research results in recent years in China involved in the effects of Bt transgenic crops (Bt transgenic cottons and rice) on soil ecosystems were summarized with special attentions paid to the release and persistence of Bt toxins, and the toxicology to microorganisms, as well as the change of soil biochemical properties in soils where Bt transgenic crops were planted or incubated with their biomass. In addition, the complexity and current research defaults of ecological risk evaluation of Bt transgenic crops in China were highlighted.