In this work, two polysaccharide nanocrystals-rod-like cellulose whisker (CW) and platelet-like starch nanocrystal (SN) were individually incorporated into an aliphatic thermoplastic polyester to produce biodegradable poly(butylene succinate) (PBS)/nanocrystals biocomposites. At loading levels of 2 wt% CW or 5 wt% SN the PBS-based nanocomposites showed simultaneous enhancement of strength and elongation compared to the neat PBS. This was primarily attributed to the uniform dispersion of nanofillers and strong interfacial adhesion between filler and matrix. Nucleation of the nanocrystals, formation of a percolating network, and interaction between filler and matrix collectively contributed to the improvement of crystallinity and thermal properties of the composites. This high performance, fully biodegradable, eco-friendly nanocomposite will expand the utilization of polysaccharide nanocrystals from renewable bioresources and the practical application of PBS.