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Aromatic copolyesters, derived from bio-based nipagin and eugenol, were synthesized with renewable 1,6-hexandiol as the spacer. Number-average, weight-average molecular weights (M_n, M_w), and polydispersity (D) values were determined by size exclusion chromatography (SEC). Chemical structures were confirmed by ¹H NMR and ¹³C NMR spectroscopies. Chemical microstructure analysis suggested that the nipagin and eugenol-derived units were inserted into polymer chains in an arbitrary manner. Due to the short chain of 1,6-hexanediol, the splitting of magnetically different methylene carbons, adjacent to the alcohol-oxygens, proved to be more sensitive towards sequence distributions, at the dyed level, than those from 1,10-decanediol. Thermal gravimetric analysis (TGA) demonstrated that these polyester materials have excellent thermal stability (>360 ^oC), regardless of the content of eugenol-derived composition incorporated. Differential scanning calorimetric (DSC) and wide-angle X-ray diffraction (WXRD) experiments revealed the semicrystalline nature for this kind of copolyesters. The crystallinities gradually decreased with the increase of eugenol-derived composition. Thermal and crystalline properties were well discussed from the microscopic perspective. The point of this work lies in establishing guidance for future design and modification of high-performance polymer materials from the microscopic perspective.