High silica A-type granites (HSAGs) are important carriers of rare metal elements. Formation of HSAGs by crystal-liquid segregation would facilitate fertilization of rare metals and rare earth elements (REE). In this work, we present detailed petrology, whole-rock geochemistry, and in-situ zircon UPb ages and HfO isotopic compositions of the Halajun HSAGs in the South Tienshan Orogenic Belt (STOB). In combination with the previous study of the Halajun syenite and monzonite, we unravel the genetic connection of these granitoids and further explore the metallogenetic potentiality of HSAGs along the STOB in China. The Halajun granites have geochemical affinities of HSAGs with high SiO₂ contents (> 70 wt%), whole-rock zirconium saturation thermometry (680–860 °C), high Ga/Al ratios and high field strength elements (HFSE) contents. The HSAGs (273–279 Ma), monzonite (280 Ma) and syenite (283 Ma) have similar formation ages, identical mineral assemblages, and consistent variations in major elements, implying a common magma reservoir of their parental magma. The Tamu and Huoshibulake HSAGs have high SiO₂ (74.5–78.1 wt%) contents, low Sr (5–28 ppm) and Ba (7–60 ppm) contents, high Rb/Sr ratios (11.6–87.5), and strong negative Eu anomalies (0.01–0.08). Combined with the petrographic features, these geochemical variations suggest that they are the extracted melt. Conversely, the geochemical (high Sr and Ba concentrations, and Eu/Eu* near unity) and petrographic features of monzonite and syenite represent the residual silicic cumulate (crystals ± trapped melt). The Kezi'ertuo and Halajun II HSAGs have SiO₂ (71.9–76.5 wt%) contents, Sr (35–101 ppm) and Ba (60–541 ppm) contents, Rb/Sr ratios (1.9–8.9), and negative Eu anomalies (0.04–0.43), indicating the intermediate component (extracted melt + fractional crystals) in the consecutive system of crystal-liquid segregation. In-situ zircon HfO isotopes for the Halajun granitoids indicate a complex trans-crustal magmatic process involving crystal-liquid segregation and wall-rock assimilation. The long-time span of Tarim Large Igneous Province (TLIP) sustained injection of mantle-derived magma and/or advective heat to the magma chamber (> 1 Ma). Owing to the prolonged magma evolution, the highly fractionated silicic magma with high incompatible elements and F contents was extracted from the magma mush, and formed the HSAGs.