The nanoscale β-cyclodextrin encapsulated cinnamaldehyde inclusion complexes were fabricated by a nano spray dryer. The inclusion complexes' physical and chemical properties, encapsulation efficiency, Fourier transform infrared, release profile, particle diameter, antimicrobial and antioxidant activity, were included in this dataset. Also, its effects of postharvest preservation of rambutan, which contains fruit firmness, soluble solid content, titratable acid, sugar to acid ratio, weight loss, peel browning, and surface microbial population were recorded to develop a comprehensive dataset on nanoscale β-cyclodextrin encapsulated cinnamaldehyde inclusion complexes and preservation effects on postharvest rambutans.