To address the influence of the high-altitude low Reynolds number effect on compressors, this study investigates an axial transonic compressor through a numerical approach based on the Reynolds-averaged Navier–Stokes equations. The entropy generation loss model and the \(\gamma -{Re}_{\theta \text{t}}\) transition model are employed to analyze variations in compressor performance, flow field behavior, and flow loss under different flight altitudes. The results show that the increased flight altitude will induce a low Reynolds number effect, reducing the total pressure ratio, isentropic efficiency, peak efficiency, and compressor stall margin. Under peak efficiency conditions, the flow deflection in the rotor passage experiences a rapid decrease at altitudes above 20 km. Additionally, the separation line on the rotor suction surface and the location of the passage shock wave shift forward, leading to an expansion of the low-energy fluid range and a widening of the wake. The separation of the stator suction surface develops from a closed separation bubble at the leading edge to an open significant separation at the trailing edge. The pressure coefficient of the stator and rotor blades at the trailing edge shows a downward trend. Entropy generation increases in the spanwise and axial directions, with losses near the end walls dominating. The high-altitude low Reynolds number effect leads to a general decline in the performance of the transonic compressor and alters the flow field.