The invention discloses a calibration system for leakage detection of a fuel evaporation system and a detection method thereof. The system for leakage detection of a fuel evaporation system comprisesa calibration reference system and a leakage detection system; the calibration reference system comprises a sealed reference fuel tank, a temperature sensor, a pressure sensor, a liquid level sensor,a vacuum pump, a reference hole group, a sealed reference fuel tank controller and the like; the reference hole group is arranged on the sealed reference fuel tank, and the temperature T, the fuel liquid level H and the size D of the reference hole group are changed; the vacuum pump is used for establishing the vacuum degree for the sealed reference fuel tank to measure the pressure; and a function D=f (T, P, H) is fitted through a plurality of groups of (T, P, H, D) data. The leakage detection system measures the temperature T0 and the fuel liquid level H0, the vacuum pump of the detection system is operated in the same state as the vacuum pump of the calibration system to establish the vacuum degree for the fuel tank to be detected to measure the pressure P0, and the controller of the fuel tank to be detected is used to calculate the size D0 of the leakage hole of the fuel tank to be detected through adoption of the function so as to improve the detection precision of leakage detection of the fuel evaporation system and shorten the detection time.