A simple and sensitive method for the simultaneous quantitation of prohexadione-Ca and uniconazole in the field experiment of Oryza sativa L. and Citrus reticulata Blanco was established using solid-phase extraction (SPE) with polymer anion exchange (PAX) and Florisil followed by LC-MS/MS. The method demonstrated excellent linearity (R2 > 0.999 0), trueness (recoveries between 95~105%), precision (CVs between 0.8~12%), sensitivity, and repeatability (LOQ of 0.05 and 0.01 mg/kg, respectively). Residue tests were conducted in the field at 12 representative sites in China, revealing final concentrations of prohexadione-Ca and uniconazole in brown rice, rice hull, and rice straw to be below 0.05 mg/kg, while in whole citrus fruit and citrus pulp, they were below 0.01 mg/kg. These were below the maximum residue limits specified in China. The chronic dietary risks of prohexadione-Ca and uniconazole in rice crops and citrus fruits were calculated to be 0.48% and 0.91%, respectively. Our research suggests that the chronic risk associated with the daily consumption of rice crops and citrus fruit at the recommended dosage is acceptable.