This thesis describes synthetic and processing strategies to formulate epoxies resins with molecular heterogeneity to achieve enhanced engineering properties. The network heterogeneities include chemical differences in stiffness and crosslink density, as well as mechanical difference in baseline energy state. The focus is to understand the fundamental structure-process-property relationships in these unusual network polymers, especially the post-yield responses and fracture toughness. The main characterization techniques to probe the complex network architectures are dynamic mechanical spectroscopy and compression tests. Ductility and governing parameters are also proposed to describe the relationships between molecular structures and physical properties. Three different staged fabrication strategies are studied, with increasing complexity in network architectures. In the Topologically Heterogeneous Network approach, a rigid multi-functional prepolymer is prepared first and then reacted with flexible reagents to generate within the resulting materials regions of varying stiffness and crosslink density. In the Prestressed Double Network approach, deformation is imposed between cure reactions to alter the energy state of the resulting materials. In the Asymmetric Double Network approach, lightly crosslinked aliphatic network and highly crosslinked aromatic network are introduced as the major and minor components. All three strategies produce macroscopically homogeneous epoxies with improved toughness. Combinations of the approaches are also evaluated. The observed changes in the dynamic mechanical spectra include broadening and shifting of the transitions with imposed molecular heterogeneity. A ductility parameter based on mechanical spectroscopy is proposed to quantify the influence of segmental mobility on large strain deformation. Compression test is also investigated to extract intrinsic network characteristics of thermosets. A second ductility parameter based on equilibrium and kinematic considerations is proposed to correlate with fracture toughness. Both the glass transition temperature and cohesive energy density are correlated with the non-linear mechanical behavior, including rejuvenated stress and strain hardening modulus.