Taking the pulsating heat pipe with corrugated configuration and the microgrooved flat heat pipe as the research objects, a threedimensional unsteady mathematical model was constructed based on the Mixture model, and the reliability of the model was verified. This mathematical model was used to compare the thermal resistance, average wall temperature and the uniformity of the evaporation section wall temperature of the two types of micro heat pipes under the same heat dissipation space and heat flux. The results show that, compared with the microgrooved flat heat pipe, the pulsating heat pipe with corrugated configuration presents lower thermal resistance and better heat transfer performance; the steadystate average wall temperature of the evaporation section of the pulsating heat pipe with corrugated configuration is lower, and this advantage becomes more obvious as the heat flux increases; the pulsating heat pipe with corrugated configuration has better wall temperature uniformity in the evaporation section on the spatial scale, and this advantage is more prominent in the case of high heat flux, but this uniformity changes relatively drastically on the time scale.