Heat exchange processes in the combustion chamber of hydrogen engines, unlike engines running on traditional hydrocarbon fuels, have the features. A number of authors of experimental works note that heat losses in hydrogen engines tend to increase compared to gasoline engines. In this work, the authors put forward and proved theoretically and experimentally a hypothesis about the possibility of hydrogen flame penetration in micro-gaps in the combustion chamber. Theoretical studies of turbulent combustion processes and the local process were carried out using a 3D mathematical model based on fundamental equations of the Navier-Stokes type. The experimental studies involved direct measurement of the local heat flow in the micro-gap of a running engine using a special heat flow sensor operating on the principle of an “additional wall”. Practical recommendations have been developed to reduce heat losses in hydrogen engines. The results obtained should be taken into account when creating new, promising hydrogen engines, as well as when converting traditional engines to hydrogen.