The Bailingshan submarine volcanic-hosted iron deposit in the Eastern Tianshan provides an opportunity to investigate skarn hydrothermal evolution and high-grade Fe mineralization. This study integrates garnet petrography, in situ major- and trace-element analyses, garnet U–Pb geochronology, and amphibole ⁴⁰Ar/³⁹Ar geochronology. Four generations of grossular–andradite garnet (Grt1–Grt4) exhibit systematic textural and compositional variations reflecting the combined effects of crystal-chemical controls, hydrothermal fluid composition, and fluid–rock interaction. U–Pb dating of Grt2 yields 331.8 ± 8.9 Ma, linking the principal skarn formation and Fe mineralization stage to Early Carboniferous volcanism. Amphibole ⁴⁰Ar/³⁹Ar dating yields 302.6 ± 2.4 Ma, constraining a younger, localized hydrothermal overprint with limited Fe addition. Integrated evidence indicates that the Bailingshan deposit formed through a multistage, episodic hydrothermal evolution involving initial skarn formation, the principal Grt2–magnetite stage, subsequent shifts in hydrothermal conditions recorded by Grt3 and Grt4, and a localized late-stage hydrothermal overprint. These results not only constrain the timing of mineralization and subsequent overprinting but also offer valuable exploration implications for high-grade Fe mineralization in the Eastern Tianshan and comparable submarine volcanic-hosted iron districts.