The needle valve, serving as the flow control unit of the thruster system, is a crucial component of the entire thruster. Its performance directly impacts the flow state of the rarefied gas in the micro-nozzle structure of the cold gas micro-thruster, thereby exerting a significant influence on the high precision and stability of the propulsion system as a whole. This study examines the impact of different needle valve structures on the flow and thrust in micro-nozzles using the DSMC method. The analysis includes discussions on the spatial distribution, Kn distribution, slip velocity distribution, and pressure distribution of the micro-nozzle’s flow mechanism. Notably, increased curvature of the needle valve enhances the flow velocity in the throat and expansion section. The magnitude of the curvature directly affects the flow velocity, with larger curvatures resulting in higher velocities. Comparing different spool shapes, the conical spool shape minimizes the velocity gradient in the high-speed region at the junction between the spool area and the outlet pipe, particularly with a wide opening. Increasing the curvature of the spool leads to a higher velocity in the expansion section. Consequently, an arc-shaped spool valve maximizes the nitrogen flow at the nozzle during wide openings, thereby enhancing thrust. These research findings serve as a valuable reference for the structural design of the needle valve in the micro-nozzle of the cold gas micro-thruster.