Pyraclostrobin is one of the most prevalent strobilurin fungicides from the broad-spectrum control of fungal diseases. The ever-increasing pesticides with the active ingredient of pyraclostrobin have been put into the agroecosystem in recent years. The survival of non-targeted organisms and the by-effects on human health can be induced by pyraclostrobin biomagnification within the food web. This study aims to elaborate on the fate characteristics and risk magnitude of pyraclostrobin after large-scale application that contributed to agroecosystem sustainability and dietary rationality. The registered crops included wheat, peanut, watermelon, and cucumber in the main production areas in China. The tracing of pyraclostrobin was performed on the multiple crop matrices using the self-developed ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Some measurements were used to validate the specificity, linearity, matrix effect (ME), accuracy, precision, limit of detection (LOD), and limit of quantification (LOQ). LOD and LOQ were estimated to be 0.0001-0.0004, and 0.001 mg/kg for the wheat grains, wheat straw, peanut kernels, peanut straw, cucumber, and watermelon matrices, respectively. The average recoveries of the target analyte ranged from 81.2% to 112.2% for all fortification levels. The precision values were associated with the analytical methods. The relative standard deviations (RSD) were 0.7% to 18.1% for the pyraclostrobin in all matrices. The fate characteristics of pyraclostrobin were elucidated using the verified storage stability. Some parameters were selected to represent the occurrence, pharmacokinetics dissipation, and terminal magnitude of pyraclostrobin, including the original depositions, half-lives, and terminal magnitude. The concentrations of pyraclostrobin were attached the maximum of <0.001, ≤0.209, ≤0.048 mg/kg 2 h after the last application in peanut kernels, cucumber and watermelon, respectively, and 0.005-0.043 mg/kg 7 d after last application in the wheat grain. Significant differences were observed in the degradation dynamics of pyraclostrobin among different crops, with half-life of 1.9-4.7 d in watermelon, 2.6-7.5 d in cucumber, and 5.9-9.9 d in wheat grain. There was no half-life of peanut kernels without detecting the pyraclostrobin in any samples. The terminal level of pyraclostrobin in the wheat and peanut straws (0.187-75.291 mg/kg) was much higher than that in the edible part, including the wheat grain and peanut kernel (≤0.096 mg/kg). The long-term dietary risks of pyraclostrobin were further clarified for the population with the different regions, gender, and age using the supervised trials median residues (STMR) for the investigated crops that were recommended by the large-scale field trials. The risk quotients (RQ) were assessed as 123.959%-406.415% by the deterministic model, indicating out of the acceptable range. The risk quotients were inversely correlated to the age of the population. The children group was subjected to the greatest long-term risks of pyraclostrobin exposure from the dietary pathway. The population subgroup location in rural (RQ, 146.799%-406.415%) suffered more serious exposures than that in urban (123.959%-374.217%). A probabilistic model was further introduced for a more accurate estimation of dietary exposure. The total chronic risks (RQ) caused by consuming wheat grain and watermelon ranged from 0.025% to 11.309% from the 50 percentile to the 99.9 percentile, far less than 100%, indicating no potential risks for the population. The unacceptable chronic risk magnitude of pyraclostrobin was determined, according to the probabilistic distribution in the residual levels of the above four crops. Anyway, the hazard effects of pyraclostrobin from dietary pathways should be emphasized in daily life, especially for rural children group.