In this chapter, the fabrication, characterization, and modeling of functionally graded nanocomposites (FGNs) are presented. FGNs with phenolic matrix and synthetic graphite (SG) as nanofillers were fabricated using a combined powder stacking and compression molding techniques. Ball milling was used to homogeneously distribute nanofillers within the phenolic matrix. The process allowed FGNs with four different microstructure gradient patterns of the same geometry and SG content, as well as non-graded nanocomposites (NGNs), to be fabricated. The surface morphology of FGNs and SG distribution were examined. The transient thermal behavior of FGNs subjected to sudden temperature changes was numerically investigated to examine the effect of compositional patterns on the temperature gradient field in these materials. Temperature-dependent thermal conductivity and heat capacity of the FGN components were measured and used in finite element-based transient thermal analysis developed based on the experimental procedure. A controlled microstructure and composition was achieved in microscale. Thermomechanical and viscoelastic properties of nanocomposites were highly affected by the distribution patterns of SG within the matrix. The transient thermal analysis results showed that the transient time and temperature field in nanocomposite structures were highly influenced by the compositional gradient configurations. The FGN with a gradual decrease in reinforcing content from the exposed side to the other side had the lowest temperature gradient field (about 11 °C less than the other gradient patterns) and transient time (about 56 seconds less than the other gradient patterns)