In this study, three different substrate holder shapes—trapezoidal, circular frustum, and adjustable cyclic—were designed and optimized to enhance the quality of polycrystalline diamond films grown using microwave plasma chemical vapor deposition (MPCVD). Simulation results indicate that altering the shape of the substrate holder leads to a uniform distribution of the electric field on the surface, significantly suppressing the formation of secondary plasma. This design ensures a more even distribution of the temperature field and plasma environment on the substrate holder, resulting in a heart-shaped distribution. Polycrystalline diamond films were synthesized under these three different substrate holder conditions, and their morphology and crystal quality were characterized using optical microscopy, Raman spectroscopy, and high-resolution X-ray diffraction. Under conditions of 5 kW power and 90 Torr pressure, the adjustable cyclic substrate holder produced high-quality 3-inch diamond films with low stress and narrow Raman full width at half maximum (FWHM). The results confirm the reliability of the simulations and the effectiveness of the adjustable cyclic substrate holder. This approach provides a viable method for scaling up the size and improving the quality of polycrystalline diamond films for future applications.