Apatite occurs in diverse types of hydrothermal mineral deposits and has been widely used to constrain the nature and evolution of ore-forming fluid. The origin of ore fluids responsible for formation of iron oxide-copper–gold (IOCG) deposits remains controversial. Here we combine textural observations from optical microscopic cathodoluminescence (OM-CL) and backscattered electron (BSE) images with in situ chemical and strontium isotopic analyses of apatite in the Lanniping Fe-Cu deposit in Kangdian metallogenic province, SW China, to reconstruct the hydrothermal evolution history of this deposit. Paragenetic sequences of the deposit include pre-ore Na-alteration (stage I) of predominant albite, stage II iron-oxide mineralization with the associated Ca-Fe alteration characterized by magnetite and minor apatite, stage III Cu-Fe sulfides and the associated K-Fe alteration, and final stage IV Ca-Mg alteration. Three types of apatite at different paragenetic stages were identified in this deposit. The pristine Type 1 apatite are intergrown with stage II magnetite and show blue colors under OM-CL images. The Type 2 apatite, which are darker than Type 1 apatite under BSE images, show dark yellow CL colors. They commonly occur as metasomatized domains of Type 1 apatite and can contain chalcopyrite mineral inclusions, indicating that they are coeval products during stage III. The Type 3 apatite show bright yellow CL colors, and occur as overgrowth rims of both Type 1 and 2 apatite. The Type 1 apatite have highest REY contents (5342 to 12983 ppm) and primitive 87Sr/86Sr ratios ranging from 0.70630 to 0.71093, which overlap the associated igneous intrusions. In contrast, the Type 2 and Type 3 apatite have gradually lower REY contents (866 to 4255 ppm and 142 to 635 ppm, respectively) but higher 87Sr/86Sr ratios (0.71009 to 0.71698 and 0.71904 to 0.72602, respectively). Our data hence suggest that the ore-forming fluids were mainly magmatic-hydrothermal origin and were gradually enriched in radiogenic Sr isotope by mixing with external fluid. Our case study highlights that texturally constrained apatite could be utilized to effectively trace fluid evolution of IOCG mineralization, and by reference, other hydrothermal mineralizing systems.