Sulphur isotopes can be used as a powerful tool to trace fluid evolution and explore the formation of chimneys. To clarify the in situ S isotopic variations of sulphides at the micro-scale, we analyzed a sulphide chimney collected from the hydrothermal field in the East Pacific Rise 1–2° S using a sensitive high-mass-resolution ion micro-probe for stable isotopes (SHRIMP SI). Three mineral zones can be identified in the chimney: an external outer wall of porous anhydrite and colloform pyrite, an internal middle zone of sub-euhedral pyrite and massive chalcopyrite, and an inner zone of massive pyrite. The δ34SV-CDT values of the sulphides fall within the range 1.83–7.51 ‰ (avg. 4.05 ‰, n = 16), and S isotopic values increase from the core (3.09 ‰, n = 3) to the middle (3.78 ‰, n = 11) to the edge (6.99 ‰, n = 2). These results illustrate mineral crystallization processes and the mixing between seawater-derived S and magmatic–hydrothermal fluids during the growth of the chimney. The zones from the edge to the core are characterized by crystal morphologies of colloform/anhedral pyrite to massive pyrite with decreasing δ34S values, revealing multi-stage mineral deposition and sulphur isotopic fractionation. In contrast to the increase in δ34S values from the core to the edge in one profile (profile A), anomalously low δ34S values in fine-grained pyrite relative to chalcopyrite in another profile (profile B) in the middle zone result from S isotopic exchange between seawater SO42− and fluid H2S due to different fluid–seawater mixing, possibly caused by variations in permeability and porosity across the chimney.