AbstractAs a key dynamic element of the Bjerknes feedback mechanism, the thermocline effect (TE) is critically important to El Niño modeling. In this study, the potential influence of TE‐related parametric uncertainties on El Niño is investigated using the conditional nonlinear optimal parametric perturbation (CNOP) method based on an intermediate coupled model (ICM). The optimal perturbation of the TE‐related parameter (OTEP), which substantially affects El Niño simulations, is estimated through the CNOP approach. Results reveal that the El Niño simulation is highly sensitive to the TE uncertainty in the eastern equatorial Pacific, with OTEP‐induced simulation errors demonstrating an El Niño‐like growth trend. On one hand, as indicated by the simulated El Niño intensity, the uncertainty in the TE in the eastern region can easily affect the strength of the Bjerknes feedback‐related thermocline effect and atmospheric circulation. On the other hand, the enhanced TE is highly favored to accelerate the growth of the SST error due to the air–sea interaction, thus severely affecting the El Niño simulations. Therefore, adequately representing the TE in the equatorial eastern Pacific is emphasized for effectively improving El Niño simulations.