There may be several ecological impacts induced by transgenic cottons, apart from their direct impact on target pest. The interactions between target insect and transgenic cotton, and the way of toxic expressed by transgenic cotton varied with plant spatial parts and different growing stages are regarded as the main cause for insect to develop resistance. In transgenic cotton field, although chemicals applied to control major insect pest could be reduced greatly, insect community structure including insect pests and beneficial organisms is less stable than that of regular cotton field. It is much easier for minor insect pests developing to be major pest. In order to full utilization of transgenic cottons and keep their efficiency on target pest, methods including integrated pest management and breeding higher efficiency transgenic cottons by genetic engineering are proposed for management of pest resistance and non-target pests.