The effect of transgenic plants on the biodiversity of agroecosystem is an important environmental issue. There are many researches in this field at home and abroad recently. This paper reviewed the advances of the researches based on three levels of biodiversity as genetic diversity, species diversity and ecosystem diversity. They included following aspects: the effect of insect-resistant transgenic crops on target pest; the effect of herbicide-resistant transgenic crops on crops and wild weedy relatives; the effect of virus-resistant transgenic crops on virus; and the effect of transgenic crops on non-target organisms. This paper also discussed the effect of transgenic crops on soil ecosystem and crop genetic diversity. Their potential risks included uncontrolled flows of genes to wild relatives; development of herbicide, insect, and virus resistance in wild relatives; reduced crop genetic diversity; and adverse effects on organisms that were not pests, such as beneficial insects.