Experiments are always the go-to approach to reveal mysterious observations and verify new theories. However, scientific research has shifted to areas that are difficult to probe experimentally. Fortunately, computational approaches, such as molecular simulation, became available. With a rigorous theoretical foundation and microscopic insights, molecular simulation could explore unknown territories in physics and validate macroscopic theories. Grand challenges in petroleum engineering require knowledge at the molecular scale more than ever, such as the behavior of confined fluids in shale nanopores. Although it is widely used in materials science, biophysics, and biochemistry, molecular simulation has been underutilized in subsurface modeling. However, the complexity of the subsurface systems and the heterogeneity of reservoir fluids, which currently challenge both our continuum modeling approaches and experimental techniques, could benefit from molecular insights. In this Review, we briefly present the basics of molecular simulation and a few applications addressing current petroleum engineering challenges. These applications include (1) phase equilibria, where molecular simulation handles inaccessible experimental conditions such as high pressure, high temperature, or a toxic environment; (2) asphaltene aggregation, where molecular simulation enables the synthesis and evaluation of the solvent performance; (3) low-salinity water flooding, where molecular simulation reveals the key mechanisms; and (4) shale reservoirs, where molecular simulation derives the new physics controlling the transport phenomena in these reservoirs. Our goal is to demonstrate that the molecular models can shed some light on numerous subsurface applications, moving toward more predictive physics-based models to optimize and control subsurface systems.