Molecular simulations are currently receiving significant attention for their ability to offer a microscopic perspective that explains macroscopic phenomena. An essential aspect is the accurate characterization of molecular structural parameters and the development of realistic numerical models. This study investigates the surface morphology and elemental distribution of silicon nitride fibers through TEM and EDS, and SEM and EDS analyses. Utilizing a customized molecular dynamics approach, molecular models of amorphous and multi-interface silicon nitride fibers with complex structures were constructed. Tensile simulations were conducted to explore correlations between performance and molecular structural composition. The results demonstrate successful construction of molecular models with amorphous, amorphous–crystalline interface, and mixed crystalline structures. Mechanical property characterization reveal the following findings: (1) The nonuniform and irregular amorphous structure causes stress concentration and crack formation under applied stress. Increased density enhances material strength but leads to higher crack sensitivity. (2) Incorporating a crystalline reinforcement phase without interfacial crosslinking increases free volume and relative tensile strength, improving toughness and reducing crack susceptibility. (3) Crosslinked interfaces effectively enhance load transfer in transitional regions, strengthening the material’s tensile strength, while increased density simultaneously reduces crack propagation.