The transmitral pressure gradient is a crucial clinical indicator for diagnosing mitral regurgitation and stenosis. Numerical simulation of specific patients can obtain the complete pressure distribution in the left heart system, which is an important approach to evaluate cardiac function. However, the results are sensitive to the boundary conditions used in the numerical simulations. In the present work, we constructed a left heart model and assessed the effects of four typical boundary conditions on the transmitral pressure gradient, which is computed based on the Bernoulli equation and the line probe, respectively. The results show that the transmitral pressure gradient obtained by the line probe is sensitive to the boundary conditions. The sensitivity is closely related to the pressure in the atrium but has negligible effect on the pressure in the ventricle. This study sheds light on evaluating the pressure gradient of patient-specific treatments based on the numerical simulation of a left heart model.