UPLC-QTOF/MS technology was used to study the degradation and metabolism of chlorpyrifos during wheat growth by spraying plants with different doses of chlorpyrifos 7 days after the flowering and filling stage. We analyzed and identified chlorpyrifos metabolites in different parts of wheat in full-scan MSE mode and established a chlorpyrifos metabolite screening library using UNIFI software. The results showed that the residues of chlorpyrifos in wheat ears, leaves and stems showed a decreasing trend with the prolongation of application time, and the degradation kinetics could be fitted by the first-order kinetic equation Ct = C0 e− kt. The initial residues of chlorpyrifos in different parts of the wheat were different, which was in the order leaf > wheat ear > stem. The degradation rate of chlorpyrifos under field conditions is relatively fast, and the half-life value is 2.33–5.05 days. Chlorpyrifos can undergo a nucleophilic addition substitution reaction under the action of hydrolase to generate the secondary metabolite 3,5,6-TCP (3,5,6-trichloro-2-pyridinol). The residual amount of 3,5,6-TCP in each part of wheat showed a trend of increasing first and then decreasing over time; it reached the maximum on the 3rd, 7th or 11th day after application, and then gradually degraded. Considering that 3,5,6-TCP is a biomarker with potential threats to humans and animals, it is recommended that 3,5,6-TCP be included in the relevant regulations for dietary exposure risk assessment.