A multi-residue method for the determination of 107 pesticide residues in wolfberry has been developed and validated. Similar pretreatment approaches were compared, and the linearity, matrix effect, analysis limits, precision, stability and accuracy were validated, which verifies the satisfactory performance of this new method. The LODs and LOQs were in the range of 0.14–1.91 µg/kg and 0.46–6.37 µg/kg, respectively. The recovery of analytes at three fortification levels (10 µg/kg, 50 µg/kg, 100 µg/kg) ranged from 63.3–123.0%, 72.0–118.6% and 67.0–118.3%, respectively, with relative standard deviations (RSDs) below 15.0%. The proposed method was applied to the analysis of fifty wolfberry samples collected from supermarkets, pharmacies and farmers’ markets in different cities of Shandong Province. One hundred percent of the samples analyzed included at least one pesticide, and a total of 26 pesticide residues was detected in fifty samples, which mainly were insecticides and bactericide. Several pesticides with higher detection rates were 96% for acetamiprid, 82% for imidacloprid, 54% for thiophanate-methyl, 50% for blasticidin-S, 42% for carbendazim, 42% for tebuconazole and 36% for difenoconazole in wolfberry samples. This study proved the adaptability of the developed method to the detection of multiple pesticide residues in wolfberry and provided basis for the research on the risks to wolfberry health.