<p>This paper investigates the gas mixture flow in micro-nozzles using the direct simulation Monte Carlo method. Various binary mixtures of noble gases are employed as the working fluids. Each mixture has a mean molecular mass similar to that of pure argon. The performance parameters of micro-nozzles using these mixtures are compared with those obtained using pure argon. Results indicate that the mass flow rate, thrust, and specific impulse tend to rise with an increase in the molecular mass ratio of the mixture. Optimal performance is achieved by using the highest molecular mass ratio. For a micro-nozzle with an expansion ratio of 3, substituting pure argon with a xenon–helium mixture leads to improvements of 5.2% in mass flow rate, 7.0% in thrust, and 1.5% in specific impulse. The enhancements in mass flow rate and thrust become more pronounced with an increase in the expansion ratio. The observed improvements are primarily due to species separation, which concentrates the heavier species near the centerline and the lighter species near the side walls. Enhancing the concentration of heavier species in the high-speed core flow boosts both mass flow rate and thrust. Concentrating a low-viscosity light species, such as helium, near the side walls reduces the wall’s viscous resistance, thereby enhancing both mass flow rate and thrust. In contrast, a high-viscosity light species, such as neon, negatively impacts performance. Streamwise species separation boosts density and pressure at the outlet, positively impacting mass flow rate and thrust.</p>