The invention discloses a three-level temperature control system of an inertia measurement system. A gradient temperature difference control mode is adopted, temperature control of an inertia instrument is added on the basis of original first-level or second-level temperature control, three-level temperature control is achieved, and the three-level temperature control system controls a box body, an installing table body and the inertia instrument respectively, therefore, the influence of the outside environment temperature change on the accuracy of the inertia instrument is reduced to the maximum, the temperature gradient inside the inertia measurement system is effectively reduced through the three-level temperature control, the inertia measurement system can normally work under wide temperature environmental conditions to achieve stable working temperature, accuracy of temperature control is improved, and stabilization time of temperature control is shortened. According to the designed three-level temperature control system, a PWM temperature control mode and a digital PID temperature control mode are adopted, high antijamming capacity, stability and electromagnetic compatibility are possessed, and the temperature control system can be matched with a refrigeration fan and refrigeration modes of semiconductor refrigeration and the like for use, and is wide in application range, high in environmental adaptability, and good in stability.