A novel electrochemical sensor comprised of heteropolyacid [(NH4)12[Mo36(NO)4O108(H2O)16]·33H2O (NMo36) and molybdenum disulfide (MoS2) nanocomposites was prepared by electro-deposition for the first time, using to detect hydroquinone (HQ), catechol (CC) and resorcinol (RS). This research adopted scanning electron microscopic (SEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) techniques to character the appearance and structure features of MoS2 nanoparticles. The synergistic effect between NMo36 and two-dimensional MoS2 prompts NMo36/MoS2/GCE to possess excellent electrocatalytic activity, strong stability, fine conductivity and speedy electron transport ability, which were demonstrated by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The catalytic currents of HQ, CC and RS are enhanced on NMo36/MoS2/GCE, compared with other sensors. Furthermore, the proposed NMo36/MoS2/GCE sensor showed low detection limits (0.54 μM, 0.60 μM, 0.67 μM) and wide linear ranges (2–245 μM, 1.5–150 μM, 1.5–135 μM) for HQ, CC and RS. HQ, CC and RS were detected by the developed sensor in lake water and faucet water, and the results reveal that excellent recovery 98.42 ∼ 103.0%, which means this work has broad application prospects.