Mercury (Hg) isotopes, which display mass-dependent fractionation and mass-independent fractionation, provide a multidimensional tracer to decipher the source of metals in mineral deposits. However, mineral ore samples usually contain abundant interfering elements (e.g., Te) that can cause inaccurate Hg isotopic analysis. Available acid digestion and combustion methods failed to remove these interfering elements, hindering the application of Hg isotopes for metallogenetic tracing. Here, we developed a new dual-stage tube furnace system employing a Mn-containing catalyst tube to pretreat mineral ore samples. This method yielded good Hg recoveries (100.5 ± 3.8%, 1SD, n = 15) and low levels of interfering elements in sample solutions, allowing for accurate analysis of a series of ore standard reference materials (GBW-11108v: coal; GSO-3: Cu−Ag sulfide ore; GBW 07859: Au−Te sulfide ore). The new method was also successfully applied to measure the Hg isotopic composition of magmatic and hydrothermal ore deposits, which yielded a large range in Δ 199 Hg value (−0.19 to 0.22‰) for ore deposits formed in different geological settings, highlighting the future applications of this method for metallogenic tracing, especially tracing the source of metals in mineral ore deposits.