Although China is well-endowed with tungsten deposits, while the tungsten resources in the Central Asian Orogen Belt (CAOB) are rarely reported. Recently, many W-skarn deposits have been discovered in the East Tianshan, but the source and evolution of the mineralising fluids are poorly understood. The Xiaobaishitou W(–Mo) deposits are hosted by carbonaceous limestone or banded crystalline limestone in the Mesoproterozoic Jianshanzi Formation, which is intruded by Triassic biotite monzogranite. The deposit comprises garnet-dominated prograde skarn and retrograde skarns followed by oxides (scheelite–cassiterite–magnetite), sulphides (quartz–molybdenite–bismuthinite–pyrite–chalcopyrite–sphalerite–galena), and carbonate stages. The types of fluid inclusions are composed of liquid-rich aqueous, vapour-rich aqueous, aqueous carbon-dioxide, and daughter mineral-bearing inclusions. The homogenization temperatures of fluid inclusions change from > 400 °C in garnet, through > 380 °C in epidote and 310–280 °C in scheelite, to 280 °C in quartz and 220 °C in calcite indicating a complex magmatic-hydrothermal process. The δ18Owater values varied from + 6.1 to + 8.4‰ in garnet, + 5.2 to + 7.4‰ in epidote, + 2.0 to + 3.0‰ in quartz, to − 0.7 to − 0.1‰ in calcite. The corresponding δD values are − 95 to − 71‰ in garnet, − 84 to − 80‰ in epidote, − 115 to − 90‰ in quartz and − 101 to − 89‰ in calcite. Both O and H isotopic compositions show the mineralisation fluids are originated from deep-sourced magmatic fluids. The δ13CCO2 values in the calcite range from − 7.8 to − 7.7‰, which is characteristic of magmatic fluids interacting with reduced carbon from metamorphic rocks. The δ34S values of hydrothermal fluids range from + 4.5 to + 5.1‰, and 206Pb/204Pb, 207Pb/204Pb and 208Pb/204Pb ratios of sulphide are 18.072–18.664, 15.566–15.708, and 38.245–38.658, respectively, representing a mixed characteristic of magmatic and sedimentary sulphur. Considering the coexisting of L-type and V-type inclusions in the scheelite, we proposed that pH increase caused by fluid boiling may be the major cause for the precipitation of scheelite at the Xiaobaishitou deposit.