The non-thermal effects are considered one of the prominent advantages of pulsed field ablation (PFA). However, at higher PFA doses, the temperature rise in the tissue during PFA may exceed the thermal damage threshold, at which time intracardiac pulsatile blood flow plays a crucial role in suppressing this temperature rise. This study aims to compare the effect of heat dissipation of the different methods in simulating the pulsatile blood flow during PFA. This study first constructed an anatomy-based left atrium (LA) model and then applied the convective heat transfer (CHT) method and the computational fluid dynamics (CFD) method to the model, respectively, and the thermal convective coefficients used in the CHT method are 984 (W/m2*K) (blood-myocardium interface) and 4372 (W/m2*K) (blood–catheter interface), respectively. Then, it compared the effect of the above two methods on the maximum temperature of myocardium and blood, as well as the myocardial ablation volumes caused by irreversible electroporation (IRE) and hyperthermia under different PFA parameters. Compared with the CFD method, the CHT method underestimates the maximum temperature of myocardium and blood; the differences in the maximum temperature of myocardium and blood between the two methods at the end of the last pulse are significant (>1 °C), and the differences in the maximum temperature of blood at the end of the last pulse interval are significant (>1 °C) only at a pulse amplitude greater than 1000 V or pulse number greater than 10. Under the same pulse amplitude and different heat dissipation methods, the IRE ablation volumes are the same. Compared with the CFD method, the CHT method underestimates the hyperthermia ablation volume; the differences in the hyperthermia ablation volume are significant (>1 mm3) only at a pulse amplitude greater than 1000 V, a pulse interval of 250 ms, or a pulse number greater than 10. Additionally, the hyperthermia ablation isosurfaces are completely wrapped by the IRE ablation isosurfaces in the myocardium. Thus, during PFA, compared with the CFD method, the CHT method cannot accurately simulate the maximum myocardial temperature; however, except at the above PFA parameters, the CHT method can accurately simulate the maximum blood temperature and the myocardial ablation volume caused by IRE and hyperthermia. Additionally, within the range of the PFA parameters used in this study, the temperature rise during PFA may not lead to the appearance of additional hyperthermia ablation areas beyond the IRE ablation area in the myocardium.