Heteroatom doping is one of the most important strategies to improve the Fenton-like activity of heterogenous catalysts by optimizing the coordination environment and electronic structure of active sites. However, the doping effect on the crystal structure that governs the atom orientation and chemical stability of catalysts remains largely elusive. Here, we report the rational design and synthesis of a series of fluorine-doped MnO2 catalysts with different crystal phases (denoted as F-α-, F-β-, F-γ-, and F-δ-MnO2), aiming to reveal the crystal-dependent disparity of doping effects in PMS activation. Results demonstrate that fluorine doping exhibits selectivity towards specific crystal structures of MnO2 catalyst. The γ-MnO2 with a lowest Mn average oxidation state (AOS) significantly enhances the adsorption and activation of PMS upon fluorine doping, outperforming other MnO2 counterparts (i.e., α, β, and δ-type). Interestingly, we identify a strong linear correlation (R2 = 0.99) between the degradation rate constant variation (Δk) and ΔAOS divergence of MnO2 catalysts before and after fluorine doping, revealing a novel structure–activity relationship for Fenton-like catalysis optimization. In addition, a nonradical pathway with synergism of 1O2 and active surface-complex contributes greatly to pollutant removal in the developed F-γ-MnO2/PMS system, thereby demonstrating outstanding degradation performance towards electron-rich organics. This work provides fundamental insights into the crystal structure–activity relationship in the disparity of doping effect, which may inspire the rational design of efficient Fenton-like catalysts for wastewater treatment.