The procedures of calculating thermal insulation-layer thickness, hot and cold load, semiconductor cooling and heating capacity and corresponding electric power which were involved in designing temperature control system for missile launch canister were analyzed. A rapid method based on working condition and looking up table for estimating the semiconductor cooling capacity was proposed. The system hardware and software design was also discussed, and a new temperature control strategy for systems with multi temperature sensor and multi heat pumps that were aligned alternately as an array by using unidirectional temperature control, temperature error gradient control, PID control algorithm and other methods was presented. Tests show that the system performance such as control precision, temperature uniformity, energy efficiency and automation degree, etc. is improved relative to the existing equipment. The result has positive significance for extending the standby time and optimizing the internal environment control of launch canister. The scheme and implementing methods referred in the paper have good reference value for similar designs.