Single crystal diamond has excellent electrical properties. Heteroepitaxy is an important method for preparation of single crystal diamond. High-density and high-orientation diamond nucleation is the key to obtain heteroepitaxial large-size diamond single crystal films, and the bias-enhanced nucleation method is the main technology for high-density nucleation. COMSOL Multiphysics is used to construct a multi-physical field (plasma field, electromagnetic field, and fluid heat transfer field) coupling model. Based on the negative substrate bias, the structure substrates of the single-concave-groove, the double-concave-groove, the single-convex-groove, and the double-convex-groove are simulated respectively. In the radial direction, the radial cross section at 1 mm above the substrate surface is selected for research. In the axial direction, the axial cross sections perpendicular to the substrate at the center and both ends of the groove are selected for research. Data of the radial cross section and the axial cross sections are used to compare and analyze the influence of the substrate structure on the uniformity of plasma distribution. The accuracy of the model is verified by scanning microscope characterization of diamond heteroepitaxial bias nucleation. The simulation results show that the high-density plasma is evenly distributed at 2 mm from the center in the radial direction of the double-convex-groove structure. The plasma density at 2-5 mm from the center in the radial direction gradually decreases, and the plasma density at other positions in the radial direction approaches zero. The plasma density in the axial direction of the double-convex-groove structure is reduced by half from the center to the edge. The plasma distribution in the radial direction of the single-concave-groove structure shows that the plasma density at two ends are slightly higher than that at the center, and the electron density distribution in the axial direction is basically the same. It shows that the plasma of the double-convex-groove structure has the worst distribution uniformity in the radial and axial directions, and the plasma of the single-concave-groove structure substrate has the best distribution uniformity in the radial and axial directions. The experimental results show that the diamond nucleation does not occur at the plasma density of the double-convex-groove structure substrate approaching zero. The nucleation area and the non-nucleation area of the double-convex-groove are 37% and 63%, respectively. The double-convex-groove structure has a high density plasma region of about 40% in the radial direction. The simulated high-density plasma region and the nucleation region are almost equal. The uniform nucleation area of the double-convex-groove structure is 17%, and the uniform nucleation area of the single-concave-groove structure is 80%. The ratio of the nucleation uniform zone of the single-concave-groove structure to the double-concave-groove structure is 4.7. In the radial direction, the plasma uniform distribution areas of the single-concave-groove structure and the double-convex-groove structure are 20% and 98%, respectively. The ratio of the plasma uniform region of the single-concave-groove structure and the double-concave-groove structure is 4.9. The ratio of the simulated plasma uniform distribution area to the experimental nucleation uniform area is close to equal. Therefore, the high density plasma distribution on the surface of the sample during the bias nucleation process is conducive to diamond nucleation, and the uniform distribution of plasma on the surface of the sample is conducive to improving the uniformity of bias nucleation of diamond heteroepitaxy.