Manganese-doped zinc sulfide quantum dots (Mn-ZnS QDs) are promising candidates for multi-channel sensing analysis due to their multi-dimensional optical properties. In this study, we integrated amino-silane and ionic liquid co-modified Mn-ZnS QDs and covalent organic frameworks (COFs) into optosensing nanoparticles to provide triple-dimensional optical response signals and combined them with chemometrics for the analysis of multiple pesticide residues. Through the exploration and optimization of a series of conditions, fluorescence, room temperature phosphorescence, and ultraviolet−visible combined with chemometrics were used for the discrimination and recognition of multiple pesticide residues in fruits and vegetables. The ionic liquid of 1-vinyl-3-ethylimidazolium tetrafluoroborate was used to modify Mn-ZnS QDs to improve the optical response and enrichment of pesticide adsorption sites, which were also synergistically enhanced by the COF support. This is a potential method to discriminate pesticides efficiently and enables fast and reliable analysis of pesticides in the agricultural and food industries.