Utilizing a novel, hybrid molecular dynamics, Monte Carlo simulation, we report on microstructural changes in a polymer network that arise in response to oscillatory shear deformation. We model telechelic self-associating polymers as a course-grained, bead-spring system. The stress response of the system is obtained from rheological experiments and is reported as a function of frequency and amplitude in both the linear and nonlinear regimes. The frequency-dependent material properties are then correlated with observed changes in the topological network structure. While only minimal structural variations are observed in the elastic regime, a substantial rearrangement occurs in the low frequency, large amplitude viscous regime. Aggregates tend to break apart, resulting in an increased density of free chains. Additionally, the network tends to break and form larger structural elements with an increase multiplicity of chains bridging between the same two aggregates.