In this study, we established a matching method for a twin variable geometry turbocharging (Twin-VGT) system under varying expansion ratios at high altitudes. In addition, we developed an equivalent thermodynamic model of a two-stage variable turbine with the effective flow areas of turbines obtained under velocity constraints for altitudes ranging from 0 to 5500 m. The effects of altitudes on the matching efficacy of a two-stage compressor under different operating conditions were evaluated. Additionally, an optimal distribution of the total boost pressure was determined to minimize the output power of the two-stage compressor during non-isothermal compression at various altitudes. Furthermore, the interplay between exhaust available energy (EAE), total expansion ratio (TER), exhaust temperature, and turbine power was investigated. Lastly, the peak efficiency of the turbocharging system was evaluated by analyzing the distribution of the TER and total enthalpy drop, aimed at optimizing EAE at different altitudes.