In this study, a series of Fe-doped g-C3N4 (Fe–C3N4) samples was synthesized and characterized via X-ray powder diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflection spectroscopy (UV-vis DRS), and photoluminescence (PL) spectroscopy. The photocatalytic activity of the synthesized Fe–C3N4 was investigated toward methylene blue (MB) degradation with hydrogen peroxide (H2O2) assistance. The results showed that the Fe–C3N4 heterogeneous photo-Fenton-like system showed excellent catalytic performance when the pH value was varied from 3.0 to 9.0. Evaluating the effects of various inorganic anions in the Fe–C3N4 heterogeneous photo-Fenton-like system, HCO3− showed a dual effect on MB degradation, and Cl− and NO3− showed an inhibitory effect on MB degradation. Evaluating the effects of inorganic cations, Al3+, Mg2+, and Ca2+ strongly inhibited MB degradation. Recycling experiments demonstrated that Fe–C3N4 possesses good reusability and stability. Quenching experiments were carried out, and it was found that hydroxyl radicals (·OH) were the primary active species in the system. Besides, nine intermediates were identified via LC/MS, and a possible MB degradation pathway in the system was proposed. This study could promote the application of this Fe–C3N4 heterogeneous photo-Fenton-like system in realistic dye wastewater.