This study describes the variation in residue behavior of fluopyram in soil, carrot root, and carrot leaf samples after the application of fluopyram (41.7% suspension, Bayer) by foliar spray or root irrigation at the standard of 250.00 g active ingredient per hectare (a.i./ha) and double-dose treatment (500.00 g a.i./ha). Fluopyram and its metabolite fluopyram-benzamide were extracted and cleaned up using the QuEChERS method and subsequently quantified with LC-QQQ-MS/MS. The LOD and LOQ of the developed method were in the range of 0.05–2.65 ug/kg and 0.16–8.82 ug/kg, respectively. After root irrigation, the final residues detected in edible parts were 0.60 and 1.80 mg/kg, respectively, when 250.00 and 500.00 g a.i./ha were applied, which is much higher than the maximum residue limit in China (0.40 mg/kg). In contrast, after spray application, most of the fluopyram dissipated from the surface of carrot leaves, and the final residues in carrot roots were both only 0.05 mg/kg. Dietary risk assessments revealed a 23–40% risk quotient for the root irrigation method, which was higher than that for the foliar spray method (8–14%). This is the first report comparing the residue behavior of fluopyram applied by root irrigation and foliar spray. This study demonstrates the difference in risk associated with the two application methods and can serve as a reference for the safe application of fluopyram.