Chlorpyrifos (CPS) is an organophosphorus pesticide widely utilized in agricultural production. Much like other commonly used highly toxic and hazardous substances, is harmful to humans, plants, and animals. Thus, the development of highly efficient electrocatalysts that can monitor and detect levels of CPS in environmental samples is urgently required. This research describes a simple means of synthesizing Au nanoclusters (AuNCs) incorporated into MoSe2-Porous carbons (PCs) via a single-step hydrothermal reaction followed by chemical reduction. AuCN-MoSe2-PC coated Glassy carbon electrodes (GCEs) exhibited excellent electrocatalytic activity, interfacial charge transfer ability (96 Ω), and cathode peak intensities at a low reduction wave potential (∼-0.74 V) for sensing CPS. The developed sensor exhibited a wide linear range from 5 to 185 nM, a rapid amperometric response of < 3 s, a low detection limit (0.15 nM), and ultra-sensitivity (27.027 μA nM−1 cm−2) for CPS at −0.74 V vs. Ag|AgCl than other reported modified electrodes. Furthermore, the sensor had excellent reproducibility, repeatability, reusability, and long-time stability (88 % activity retention after 1 month) with a relative standard deviation (RSD) of < 5% and exhibited remarkable tolerance for the detection of CPS in the presence of potentially interfering substances. The practical applicability of the sensor was tested for the quantitative analysis of trace CPS levels in paddy water, pond water, and seawater samples, and it demonstrated recoveries of 97.9 to 106.6% with RSDs below 5% (n = 3), which are comparable to the results of high-performance liquid chromatography.