Knowledge on the fate of multi-pesticides in the environment is of great importance to their security use and the environmental health. In order to study the seasonal variation of pesticides pollution characteristics in the soil-groundwater system, four times of field investigation from the biggest vegetable cultivation base in China was conducted with soil and groundwater sampling from 2011 to 2012. Results showed that the composition and levels of pesticides in the greenhouse soil varied from different seasons with high levels in spring and summer. In the soil, the levels of traditional organochlorine insecticide (OCI) decreased, while that of acaricide and fungicide increased. In the groundwater, the residue of pesticide, mainly comprised of imidacloprid, was relatively steady from spring to winter. The potential environmental risks of soil were most significant in summer, while that of groundwater were mainly in summer and autumn. This suggested that much attention should be paid to pesticides monitoring and management in the greenhouse environment, especially in summer. It was also essential to monitoring groundwater pesticide in the long run.