Silicon nitride (SiNx) and silicon dioxide (SiO2) are crucial in microelectronic and photonic devices, where their interface affects performance and reliability. This study explores the effects of growth conditions on the mechanical properties of amorphous SiNx films on SiO2 substrates using molecular dynamics simulations. We address key integration challenges, focusing on mechanical residual stresses and surface defects. We assess the impact of substrate temperature, atom bombardment energy, and SiNx composition on intrinsic stress, Young’s modulus, and film toughness, focusing on the film’s susceptibility to failure and cracking. Our analysis includes deposition simulations at room temperature and 1100 K, with kinetic energies from 0.01 eV to 1 eV per atom. We investigate SiNx compositions from Si-rich to N-rich compositions to evaluate their effect on mechanical properties. The Tersoff potential for multi-body interactions facilitates a comprehensive examination of factors influencing mechanical stress and cracking. We numerically reproduced SiNx films with intrinsic stress values from 1 GPa tensile to −0.6 GPa compressive by varying deposition energy. For tensile films, we calculated critical thicknesses at which cracking occurs, from 200 nm to 4 µm. These insights refine deposition techniques, enhance mechanical durability, and support the development of reliable SiN optical platforms for photonic integrated circuits.