A modified QuEChERS method coupled with LC-MS/MS was developed and validated to detect 31 pesticides in wolfberry. The conditions for extraction solvent and QuEChERS purification were optimized. The validated method was applied to analyse pesticides in 200 wolfberry samples. The risk from chronic and acute dietary intake of the detected pesticide residues was assessed by the acceptable daily intake (ADI) and acute reference dose (ARfD), respectively, and the cumulative intake risk posed by the detected residues was assessed by the hazard index (HI). The results showed that 23 pesticides were detected in all wolfberry samples. The risk from chronic dietary intake was between 0.0001% and 1.6067%, and the risk from acute dietary intake was between 0.0010% and 0.4999%, which were all far below 100%. The HI was 0.02569 for chronic dietary intake and 0.015164 for acute dietary intake, which were both far below 1. The results indicated that the pesticide residues in wolfberry would not cause potential risk to human health. This work not only enhances our understanding of the potential exposure risks of pesticide residues in wolfberry, but also provides an effective method for the risk assessment of pesticide residues in other agricultural products.