The MC method has been published in the SAE J2601 refuelling protocol to safely and quickly refuel hydrogen fuel cell vehicles. This article adopts a dual-zone dual-temperature model that distinguishes the hydrogen temperature from the tank wall temperature to replace the dual-zone single-temperature model of the original MC method. A model (0D1D) of lumped parameter gas (0D) and one-dimensional tank wall (1D) is established simultaneously to verify the modified MC method and generate simulation data. A modified formula to the original MC method for calculating final hydrogen temperature is derived, which contains a correction factor K. The formula and coefficients of the correction factor K are determined by fitting the simulated data from the 0D1D model. The correction factor K is expressed in a piecewise function. The formulas of K are relatively complicated, so another simpler correction factor k is derived, which is a linear function. Research shows that the modified MC method extends its applicability to situations of refuelling times <30 s, while the original MC method is unsuitable. In the conditions set in this article of ambient temperature 0 to 40 °C, precooling temperature −40 to −20 °C and initial pressure 2 to 60 MPa, the modified MC method reduces the errors of final hydrogen temperature between the 0D1D model by 2 to 7 °C compared to the original one, thus improving the calculation accuracy of the pressure target and reaching a more accurate state of charge. In a word, the modified MC method improves the accuracy of refuelling control and has positive significance for the operational safety of hydrogen refuelling stations and the driver's refuelling experience.