To efficiently disperse micro/nano thermally conductivity (TC) fillers without pretreatment is still considered as a major technical issue to prepare high TC polymeric composites. Here, a new bio-based epoxy thermoset (BE) that contains the Schiff base structure was synthesized. BE/GNP (graphite nanoplatelets) powder with microcapsule structure was constructed by a grinding process, and its nanocomposites were then fabricated by hot-press technique. The relationship between GNP dispersion and TC of BE/GNP nanocomposites were systematically investigated. Results showed that the dispersion of GNP was enhanced significantly and TC network was constructed efficiently. The nanocomposite exhibited a higher TC (2.21 Wm−1K−1) with only 10 wt% of GNP content, which is ~10 fold higher than that of conventional epoxy (EP). Moreover, modified Hashin-Shtrikman model demonstrated that its thermal resistance (0.031 m2KW−1) can be decreased efficiently by ~30.8% lower than EP/GNP nanocomposites (0.0448 m2KW−1) based on this strategy. The prepared nanocomposite is used as the heat sink of LED chips, which shows potential practicability in thermal management. In addition, the Schiff base BE/GNP nanocomposite network could be degraded completely, and GNP could be nearly nondestructive recycled. This work may open up future opportunities to directly incorporate thermal conductive filler without pretreatment to fabricate “green” and highly thermal conductive polymeric composites.