Magnetite from hydrothermal deposits may show compositional zoning with various mineral inclusions in response to the evolution of hydrothermal fluids. Magnetite from the Fenghuangshan Cu-Fe-Au skarn deposit (eastern China) is a common mineral formed in the earlier stage of skarnization. Magnetite grains have dark gray and light gray zones and contain diverse mineral inclusions. Dark gray zones have higher Si, Ca, Al, and Mg contents than light gray zones. The magnetite matrix from dark gray zones shows superstructure along the [0–11] zone axis in fast Fourier transform patterns, different from magnetite in light gray zones with normal structure. Three types of mineral inclusions are identified within magnetite: nano-, micron- and submicron-nanometer inclusions. Nanoinclusions hosted in dark gray zones are actinolite, diopside, and trace element-rich magnetite, and these are likely formed by growth entrapment during magnetite crystallization at the skarn stage. The chain-width order-disorder intergrowths of diopside nanoinclusion likely indicate fluctuating fluid compositions in a lattice scale. Submicron to nanometer inclusions at the boundary between dark gray and light gray zones are quartz, titanite, and Ti-rich magnetite, which were formed via a dissolution and re-precipitation process at the quartz-sulfide stage. Micron-inclusions randomly distributed in both dark and light gray zones include calcite, ankerite, quartz, and chlorite, and these were formed via penetration of fluids at the carbonate stage. Zoned magnetite was formed by fluid replacement, overgrowth, and fluid infilling. Our study highlights the importance of mineral inclusion assemblages, and textural and chemical zonation of magnetite in constraining fluid evolution.