The presence of pesticide residues in tea has garnered increasing scholarly attention. Following the withdrawal of highly toxic pesticides from the market, there is a pressing need for alternative solutions to mitigate pest and disease occurrences in tea plantations. This study focuses on the neonicotinoid chiral pesticide of Paichongding(IPP), which possesses two chiral centers and four distinct isomers. We investigated the selective degradation of Paichongding isomers during the fermentation of Puer tea, tracking intermediate metabolites throughout the process. Using Density Functional Theory (DFT), we estimated the potential active sites of Paichongding and evaluated the toxicity of its intermediate products. Our findings indicate that Paichongding undergoes diastereo-selective degradation during Puer tea fermentation, resulting in the identification of seven key intermediates. Computational analysis revealed that the primary reaction sites of Paichongding are located on the imidazole and tetrahydropyridine rings. Toxicity assessments demonstrated that the metabolites exhibited heightened toxicity towards human genetic material, respiratory functions, and small aquatic organisms.