Organophosphorus (OPs) compounds have received enormous attention due to high neurotoxicity. However, the complex detection environment makes it very difficult to detect the OPs compounds at extremely low‐concentration. Therefore, it is vital to develop a high sensitive analytical method for the detection of low‐concentration OPs compounds at complex environment. Here, we proposed a novel surface‐enhanced Raman scattering (SERS) substrate based on the core‐shell structure Au@ZrO2 for the detection of extremely low‐concentration OPs compounds. By using above SERS substrate, we tested different kinds of OPs compounds and obtained excellent detection results. The detection limit of methyl parathion and triazophos can reach 0.01 mg/kg. Meanwhile, under the actual system (orange peel), the detection limit of the methyl parathion and triazophos also can reach 0.5 and 0.1 mg/kg, respectively. In addition, the above substrate is also very effective for the detection of dimethyl methylphosphonate (DMMP), a simulant for the chemical warfare agent (sarin), and the detection limit can reach 100 mg/kg. Besides, we also verified the reproducibility and stability of Au@ZrO2, which showed excellent properties. The relative standard deviation (RSD) of the SERS signal intensity for 20 tests was 6.38% and the enhancement ability of Au@ZrO2 can remain stable within 30 days. These results show that the proposed Au@ZrO2 SERS substrate has great potential in the detection of OPs compounds at extremely low‐concentration in the complex detection environment.