In order to meet the requirements of output torque, efficiency and compact shape of micro-spindles for small parts machining, a two-stage axial micro air turbine spindle with an axial inlet and outlet is proposed. Based on the k-ω turbulence model of SST, the flow field and operation characteristics of the two-stage axial micro air turbine spindle were studied using computational fluid dynamics (CFD) combined with an experimental study. We obtained the air turbine spindle under different working conditions of the loss and torque characteristics. When the inlet pressure was 300 KPa, the output speed of the two-stage turbine was 100,000 rpm, 9% higher than that of a single-stage turbine output torque. The total torque reached 6.39 N·mm, and the maximum efficiency of the turbine and the spindle were 42.2% and 32.3%, respectively. Through the research on the innovative structure of the two-stage axial micro air turbine spindle, the overall performance of the principle prototype has been significantly improved and the problems of insufficient output torque and low working efficiency in high-speed micro-machining can be solved practically, which laid a solid foundation for improving the machining efficiency of small parts and reducing the size of micro machine tool.