Chitin nanocrystal is a biocompatible and biodegradable nanofiller, with great potential in enhancing the mechanical and biological properties of polymers. Poly(caprolactone-diol citrate) is a kind of citrate-based biodegradable elastomer prepared by an additive-free melt polycondensation of polycaprolactone-diol and citric acid coupled with subsequent thermocuring. Here, a facile casting/evaporation method was utilized to prepare full biodegradable poly(caprolactone-diol citrate)/chitin nanocrystal nanocomposites, and their structure and properties were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, uniaxial tensile test, dynamic mechanical analysis, surface wettability and swelling analysis, thermogravimetric analysis, in vitro degradation, and cytocompatibility test. The results showed the chitin nanocrystals were uniformly distributed in the poly(caprolactone-diol citrate) matrix; with increasing chitin nanocrystal loading, the tensile modulus and strength significantly increased; furthermore, the incorporation of chitin nanocrystals endowed the poly(caprolactone-diol citrate) with more hydrophilicity, lower swelling in phosphate buffered saline solution, slow degradation rate, and greatly improved cytocompatibility. Thus, the chitin nanocrystal was a good bio-based nanofiller that could be used to tune the properties of poly(caprolactone-diol citrate) degradable bioelastomer.