Abstract The rapid increase in the economic importance of germanium (Ge) is driving further study of its geological cycle and the factors controlling its concentration in minerals. The emerging LA-ICP-MS analytic technique is playing a significant insight into the geochemical characteristics of sphalerite. In this study, LA-ICP-MS and SEM analyses were carried out, aiming to constrain the substitution mechanisms of Ge and related trace elements and to trace the evolution of hydrothermal fluids. LA-ICP-MS element mapping and SEM study showed that no Ge-bearing micro-minerals are observed in the Lehong deposit. All spot analysis data indicate notable binary correlations between Cu and Ge and between Ag and Sb, which suggests that the coupled substitutions are 3Zn2+ ↔ 2Cu+ + Ge4+ and 2Zn2+ ↔ Ag+ + Sb3+. Additionally, the monovalent elements, i.e., Cu and Ag, approximately equal to the sum of all trivalent and tetravalent elements; thus, we consider that the monovalent cations may provide the charge-balance in all of the coupled substitutions responsible for incorporating a wide range of trivalent and tetravalent cations, especially In, Sn, Sb, and Ge, in sphalerite at Lehong. The trace elements in sphalerite from two hydrothermal stages in the Lehong deposit differ significantly. Early red-brown sphalerite is more enriched in Fe, Ge, Cu, Sb and Ag than late yellow-brown sphalerite, suggesting that trace elements in sphalerite may have the potential to record the evolution of hydrothermal fluids. Early sphalerite is rich in Fe and Ge simultaneously, which points toward coupled behavior of Fe and Ge. In situ LA-ICP-MS data from sphalerite at Lehong show that the Cu contents in all samples are nearly double those of Ge. Copper enriched in early sphalerite is an essential factor to promote the substitution of Ge, which results in the coupling of Fe and Ge in sphalerite during the evolution of hydrothermal fluids. In addition, sphalerite at depth is more enriched in Mn, Ge, Cu and Cd than shallow sphalerite. There is a clear upward trend among Mn, Ge, Cu and Cd in sphalerite with increasing depth at Lehong. This relationship may be applied for exploration targeting.