The effect of pumping laser intensity uniformity (PLIU) on the operation of a hybrid optically pumped comagnetometer operating in the spin‐exchange relaxation‐free regime (SERF) regime is investigated in this paper. First, an analytical steady‐state output model for the comagnetometer with two alkali‐metal atoms and one noble‐gas atom is presented. By varying the diameter of the pumping laser beam to control the PLIU, 3D distribution models of the electron spin and nuclear spin polarization under different PLIU conditions are obtained. In the experiment, the effects of PLIU on multi‐parameter, low‐frequency magnetic‐noise suppression capability, and long‐term stability of the SERF comagnetometer are studied. The results indicate that within a certain range, increasing the diameter of the pumping laser beam improves the polarization uniformity of the atomic ensemble and reduces the light shift of the comagnetometer. As a result, both the low‐frequency magnetic noise suppression capability and the long‐term stability of the system increase. However, further reduction of the pumping laser diameter leads to a reversal of the system performance metrics, suggesting the presence of a tipping point. The research presented in this article is critical for advancing the efficient polarization study and hyperpolarization of SERF comagnetometers.