Numerical simulations were performed to study the influence of the inside diameter of the pulse separation device port on the flow features and the local heat transfer characteristics in a dual pulse solid rocket motor. A lower–upper symmetric Gauss–Seidel implicit dual time-stepping method was applied to address the problem of unsteady flow. A high-resolution upwind scheme (AUSMPW+) and Menter’s shear stress transport turbulence model were employed to solve the Reynolds-averaged Navier–Stokes equations. The conjugate heat transfer strategy was realized by enforcing a common temperature and heat flux at the fluid–solid interface. After validating the accuracy and reliability of the numerical algorithm by comparison with experimental cases, the internal flow of a dual pulse solid rocket motor was simulated. The results show that the magnitude of the velocity, the wall shear stress, and the turbulent kinetic energy downstream of the pulse separation device port decrease with increasing pulse separation device port diameter. The local heat transfer coefficient increases sharply downstream of the pulse separation device port, reaching a maximum within 1–2 diameters downstream of the pulse separation device port, before relaxing back to the fully developed pipe flow value. The peak value of the local heat transfer coefficient reduces as the pulse separation device port diameter increases. Meanwhile with an increasing pulse separation device port diameter, the position of the peak local heat transfer coefficient moves upstream to the head of the first pulse chamber, and appears upstream of the position of the reattachment point by an average of about 28.6%.