The Zijinshan high-sulphidation Cu-Au deposit located in the west Fujian Province is the largest active gold mine in China with total production of gold over 300 tonnes to date. The high-sulphidation ore bodies are characterized by the upper supergene Au and lower hypogene Cu zones bounded roughly by the paleowater table near 600 m elevation. Au-bearing goethite and limonite are the main ore minerals in the supergene zone whereas the hypogene Cu mineralization is dominated by covellite and anilite (or digenite) with minor enargite. The expected porphyry mineralization that coupled with Zijinshan is so far not exposed even to a depth of 1500 m from surface. However, the Luoboling Cu-Mo deposit which occurs only 3 km NE to Zijinshan is identified as a typical porphyry deposit. Current debate centered on whether the Zijinshan high-sulphidation epithermal deposit and the adjacent Luoboling porphyry deposit are genetically linked or discrete hydrothermal systems. Recent deep exploration at Zijinshan revealed an extension trend of Cu ore bodies and quartz-alunite alteration zone toward SE below 0 m elevation. This contradicts previous considered NE trend above 0 m elevation. In this study, fluid inclusion mapping based on rigorous strategy and sample selection was carried out on 20 sample suites scattered over the whole high-sulphidation Cu-Au ore bodies from −450 to 800 m elevation. Aqueous fluid inclusions of unambiguous primary origin in syn-ore miarolitic quartz, coarse-grained alunite crystals and quartz overgrowth zones were measured. Microthermometry results show the average Th and salinity of each sample suite ranging from 205 to 304°C and 2.4 to 5.5 wt% NaCl equiv., respectively. Both fluid temperature and salinity exhibit negative correlation with increasing elevation, indicating convective cooling by mixing and circulating of meteoric water has involved. The good consistence of mineralization distribution pattern and fluid evolution trend implies that the southeastward extending ore bodies probably reflect the fluid pathway which is connected to the deeper porphyry mineralization and their magmatic source. Considering the temperature condition (370–400°C) required for brittle-plastic transition which commonly characterizes porphyry deposits, the potential porphyry mineralization coupled to Zijinshan should have occurred at greater depth under higher temperature. Combined with recent exploration progress and the fluid evolution pattern, we therefore proposed that the Luoboling porphyry Cu-Mo deposit and the Zijinshan high-sulphidation Cu-Au deposit are likely discrete hydrothermal systems, and future porphyry deposit exploration at the deep SE segment of Zijinshan is recommended.