Zoning texture in sphalerite has been described in many studies, although its genesis and ore formation process are poorly constrained. In this investigation, we compare the in situ trace element and isotopic composition of colour-zoned sphalerites from Nayongzhi, South China, to explain the zoning growth process. Petrographic observations identified two broad types of zoned sphalerite, core–rim (CR) and core–mantle–rim (CMR) textures. Each zoned sphalerite displays two or three colour zones, including brown core, light colour bands and/or pale-yellow zones. In situ laser ablation inductively coupled plasma mass spectrometry trace-element analyses show that the three colour zones display variable trace-element compositions. Brown cores exhibit distinctly high Mn, Fe, Co, Ge, Tl and Pb concentrations, whereas pale-yellow and light colour zones have elevated Ga, Cd, Sn, In and Sb concentrations. Copper, Sb, In and Sn show slight variations between pale-yellow and light zones, the latter having higher In and Sn, but lower Cu and Sb abundances. Given the low concentration range of Pb, Ge, Tl, Mn Sb, Cd, etc., the colour of sphalerite is attributed mainly to Fe compositional variation. The δ34S values of sphalerite from Nayongzhi range from +22.3 to +27.9‰, suggesting reduced sulfur was generated by thermochemical sulfate reduction of marine sulfate in ore-hosted strata. Single-crystal colour-zoned sphalerite exhibits intracrystalline δ34S variation (up to 4.3‰), which is attributed to the δ34S composition of H2S in the original fluid. The lack of correlation between trace elements and δ34S values indicates episodic ore solution influxes and mixes with the reduced sulfur-rich fluid derived from the aquifers of the ore-hosted strata, which play a key role in the formation of the zoned Nayongzhi sphalerite. In conclusion, in situ trace element and S isotope studies of zoned sphalerite crystals might provide insight into the ore-forming process of MVT deposits.