Ultra-performance convergence chromatography is an environmentally-friendly analytical method that uses dramatically reduced amounts of organic solvents. In addition, a robust and highly sensitive chiral separation method was developed for the novel chiral acaricide cyflumetofen by using ultra-performance convergence chromatography coupled with tandem mass spectrometry, which shows that stereoisomer recoveries determined for various apple parts ranged from 78.3% to 119.9%, with the relative standard deviations being lower than 14.0%. The half-lives of (−)-cyflumetofen and (+)-cyflumetofen obtained under 5-fold applied dosage equal to 22.13 and 22.23 days, respectively. For 1.5-fold applied dosage, the respective values were determined as 22.42 and 23.64 days, i.e., the degradation of (−)-cyflumetofen was insignificantly favored over that of its enantiomer. Importantly, cyflumetofen was unevenly distributed in apples, with its relative contents in apple peel, peduncle, and pomace equal to 50%, 22%, and 16%, respectively. The proposed method can be used to efficiently separate and quantify chiral pesticide with advantages of a shorter analysis time, greater sensitivity, and better environmental compatibility. Additionally, the consumption of apples with residue of cyflumetofen did not pose a health risk to the population if the cyflumetofen applied under satisfactory agricultural practices after the long-term dietary risk assessment.