A mathematical model of single-stage thermoelectric refrigeration system (SSTRS) was built considering the influence of external heat transfer. Based on the relationship between the input system design variables and the output cooling capacity, the coefficient of performance and the influence of the fluctuation of the design variables on the stability of the thermoelectric refrigeration system output performance parameters were studied using a moment-independent sensitivity analysis. The Latin hypercube sampling method was used to simulate the fluctuation of the design variables, and their moment-independent sensitivity indices were calculated by the Monte Carlo method. The design variables were then sorted according to their importance to the output parameters, and the key design variables affecting the coefficient of performance and the cooling capacity were obtained. These results can provide useful guidance for the design and optimisation of SSTRS.