The mechanical properties of cementitious materials injected by epoxy have seldom been modeled quantitatively, and the atomic origin of the shear strength of polymer/concrete interfaces is still unknown. To understand the main parameters that affect crack filling and interface strength in mode II, we simulated polymethylmethacrylate (PMMA) injection and PMMA/silica interface shear deformation with Molecular Dynamics (MD). Injection simulation results indicate that the notch filling ratio increases with injection pressure (100 MPa–500 MPa) and temperature (200 K–400 K) and decreases with the chain length (4–16). Interface shear strength increases with the strain rate (1×108 s−1–1×109 s−1). Smooth interfaces have lower shear strengths than polymer alone, and under similar injection conditions, rough interfaces tend to be stronger than smooth ones. The shear strength of rough interfaces increases with the filling ratio and the length of the polymer chains; it is not significantly affected by temperatures under 400 K, but it drops dramatically when the temperature reaches 400 K, which corresponds to the PMMA melting temperature for the range of pressures tested. For the same injection work input, a higher interface shear strength can be achieved with the entanglement of long molecule chains rather than with asperity filling by short molecule chains. Overall, the mechanical work needed to break silica/PMMA interfaces in mode II is mainly contributed by van der Waals forces, but it is noted that interlocking forces play a critical role in interfaces created with long polymer chains, in which less non-bond energy is required to reach failure in comparison to an interface with the same shear strength created with shorter polymer chains. In general, rough interfaces with low filling ratios and long polymer chains perform better than rough interfaces with high filling ratios and short polymer chains, indicating that for the same injection work input, it is more efficient to use polymers with high polymerization.