The rapid detection of organophosphorus pesticide residues in food is crucial to food safety. One type of novel, magnetic, molecularly-imprinted polymeric microsphere (MMIP) was prepared with vinyl phosphate and 1-octadecene as a collection of dual functional monomers, which were screened by Gaussian09W molecular simulation. MMIPs were used to enrich organic phosphorus, which then detected by fluorescence quenching in vinyl phosphate-modified carbon dots (CDs@VPA) originated from anhydrous citric acid. MMIPs and CDs@VPA were characterized by TEM, particle size analysis, FT-IR, VSM, XPS, adsorption experiments, and fluorescence spectrophotometry in turn. Through the fitting data from experiment and Gaussian quantum chemical calculations, the molecular recognition properties and the mechanism of fluorescence detection between organophosphorus pesticides and CDs@VPA were also investigated. The results indicated that the MMIPs could specifically recognize and enrich triazophos with the saturated adsorption capacity 0.226 mmol g−1, the imprinting factor 4.59, and the limit of recognition as low as 0.0006 mmol L−1. Under optimal conditions, the CDs@VPA sensor has shown an extensive fluorescence property with a LOD of 0.0015 mmol L−1 and the linear range from 0.0035 mmol L−1 to 0.20 mmol L−1 (R2 = 0.9988) at 390 nm. The mechanism of fluorescence detection of organic phosphorus with CDs@VPA sensor might be attributable to hydrogen bonds formed between heteroatom O, N, S, or P, and the O−H group, which led to fluorescent quenching. Meanwhile, HN−C=O and Si−O groups in CDs@VPA system might contribute to cause excellent blue photoluminescence. The fluorescence sensor was thorough successfully employed to the detection of triazophos in cucumber samples, illustrating its tremendous value towards food sample analysis in complex matrix.