In this study, the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, combined with high-performance liquid chromatography–tandem mass spectrometry, was chosen for detecting pydiflumetofen residues in soybean plants, soybeans and soil, and assessing the risk of short- and long-term dietary intake. Pydiflumetofen concentrations ranging from 0.001–0.5 mg/L exhibited good linearity (r > 0.997). At varying doses, the average pydiflumetofen recovery rates and relative standard deviations among soybean plants, soybeans, and soil ranged from 83.9 ± 1.1% to 99.5 ± 3.3% and from 0.77 to 7.77%, respectively. The sensitivity, accuracy, and precision of the chosen methodology met the requirements of pesticide residue analysis. The results of the degradation dynamics test showed that the half-life of pydiflumetofen (t1/2) in soybean plants and in soil were 3.6 to 5.7 and from 7.9 to 25.7 d, respectively. Assessment of the concentration of pydiflumetofen residues in soybeans revealed acute and chronic dietary exposure risks of 0.06 and 7.54%, respectively. As these values are very low, pydiflumetofen residues in soybeans present an acceptable risk to public health. The results of this study will help to guide the practical application of pydiflumetofen and minimize the environmental risks associated with its use.