The invention discloses a refrigeration control method and system of a thermoelectric container. The method comprises the following steps: acquiring the internal temperature T1 of the thermoelectric container; if that the temperature T1 is higher than a preset high temperature is determined, controlling the supply voltage of a refrigeration plate of the thermoelectric container at a full voltage; if that the temperature T1 stays within a preset temperature reduction range is determined, controlling the supply voltage of the refrigeration plate at a first lower voltage; and if that the temperature T1 stays within a preset holding temperature range is determined, controlling the supply voltage of the refrigeration plate at a second lower voltage, wherein the first low voltage is less than the full voltage and greater than the second low voltage. According to the invention, by acquiring the internal temperature T1 of the thermoelectric container and controlling the value of the supply voltage of the refrigeration plate of according to the temperature T1, frequent control of the on and off of the refrigeration plate is avoided, the on-off frequency of the refrigeration plate is effectively reduced, the internal temperature of the thermoelectric container is evener, temperature fluctuation is reduced, the service life of the refrigeration plate is prolonged, and meanwhile noise and energy consumption are effectively reduced.