In this work, a satellite heat pipe operated with the ammonia and methanol are investigated for the multi objective optimization. Optimization results are used for the comparative analysis of both the heat pipe. Optimization problem of the heat pipe is formed considering minimization of the thermal resistance and total mass of heat pipe and solved using the heat transfer search algorithm. An application example of satellite heat pipe is presented, and results are obtained in the form of Pareto-optimal points. Seven geometric parameters which include the length of evaporator and condenser section, tube wall thickness, vapor core diameter, mesh number of wick, thickness of wick, and diameter of wick wire are investigated in the optimization study. Further, the effect of condenser temperature, heat load, and length of the adiabatic section on ammonia and methanol heat pipe is explored and discussed. Furthermore, the effect of the design variables and its sensitivity to performance parameters of the heat pipe are also presented. Comparative results revel that, for any given value of the total mass of heat pipe, 82.17-57.16% lower thermal resistance is observed with the ammonia heat pipe as compared to methanol heat pipe. Finally, uncertainty propagation analysis of the obtained Pareto solutions are carried out with the different uncertainty levels and observed that the results have relatively good robustness performance for uncertainty less than 5%.