The trachyte-hosted Zhujiayuan deposit is located in the North Daba Mountain of South Qinling, China. In this deposit, the presence of different stages and genetic types of biotite, apatite, and rutile make it an excellent locality to constrain the mineralization process of Nb-REE in the alkaline igneous rock. In this study, supported by electron probe microanalyzer (EPMA), chemical analyses of biotite, apatite, rutile, columbite-group minerals, fersmite, monazite, and aeschynite-group minerals were presented. Three types of biotite were identified, including magmatic (Bt-1), reequilibrated (Bt-2), and hydrothermal biotite (Bt-3). Apatite can be divided into two types: magmatic (Ap-1) and hydrothermal apatite (Ap-2). Rutile can also be divided into two types: magmatic (Rt-1) and hydrothermal rutile (Rt-2). Rt-1 and Ap-1 contain average 1.44 wt% Nb 2 O 5 and 4.14 wt% LRE 2 O 3 , respectively, indicating that certain concentrations of Nb and REE were incorporated into the rutile and apatite, respectively, during the magmatic crystallization process. The distributions of the columbite-group, fersmite, monazite, and aeschynite-group minerals, as well as the compositional characteristics of monazite, indicate the important role of hydrothermal metasomatism during Nb-REE mineralization. The compositional characteristics of Bt-2 indicate relatively high F and Cl fugacities in the hydrothermal fluid. Bt-2 and Bt-3 both have higher Nb 2 O 5 content than Bt-1, indicating a higher Nb content in the fluid. The source of fluidic Nb likely derived from the metasomatism of magmatic rutile. The REE content decreased from Ap-1 to Ap-2, possibly due to a dissolutionreprecipitation process. The compositional changes from Bt-1 to Bt-3 and Ap-1 to Ap-2 also revealed a decrease in temperature, increase in oxygen fugacity, and increase in Ca content from the magmatic to the hydrothermal system. We speculate that rutile and apatite may have originally formed from an Nb-REE-rich alkalinesilicate melt derived from the metasomatized mantle, which led to the initial Nb-REE enrichment. Subsequent hydrothermal alteration by hydrothermal fluids rich in F and Cl, accompanied by changes in the above physical and chemical conditions and fluid composition, caused a relatively limited and localized remobilization of Nb-REE into the fractures and vesicles in the trachyte.