Hydrogen is the most promising way for energy carrier because it has fast combustion velocity, the wide range of sources and the cleaning of combustion products. The hydrogen internal combustion engine (HICE) with turbocharger has been used to solve the contradiction of the power density and controlling NOx. However, the selection of the compressor for HICE with turbocharger is very different from the traditional engines because of the gas fuel. Hydrogen as the gas fuel takes the cylinder volume, which will increase the pressure and reduce the mass flow rate of air in the cylinder. Thus, this paper put forward a new method for the HICE with turbocharger taking into account of the effect of hydrogen in the cylinder. This method can calculate the turbocharging pressure ratio and the mass flow rate of air through the target power and the general parameters such as the displacement of cylinder, the intake temperature of hydrogen and the equivalence ratio of the mixture. To improve the accuracy, this method gives a series of intake temperatures of air before calculated. Then using the calculation results of the compressor outlet temperatures compare with hypothesis temperatures to get the more accurate results. To validate the correctness of this method, this paper selects a fit compressor for a 2.3L HICE and test the engine at 2000r/min and 3400r/min. Comparing the experiment data of turbocharging pressure ratio and the mass flow rate of air with the calculation results, the error between them is below than 5%, which can be accepted. This method can be used to guide the design and selection for the compressor of HICE.