Phytate, an anti-nutritional factor in Cinnamomum camphora seed kernel protein isolate (CPI), chelated with minerals and proteins to form complexes that reduced their bioavailability. The study aimed to evaluate the effects of phytase treatment on the structural and functional properties and in vitro digestibility of CPI. The results showed that the degree of phytate degradation was improved with the increase in phytase treatment time. Most of the original secondary structures were retained in the treated CPI samples. The removal of phytate increased the Zeta potential of CPI, and the protein isoelectric point was increased. Low phytate CPI samples showed higher thermal stability and higher Ca2+ content. In terms of functional properties, foaming capacity was positively correlated with phytate content, whereas foam stability, emulsifying activity index and emulsion stability index were negatively correlated with phytate content. The reduction of phytate content had a positive effect on in vitro gastrointestinal digestion, and the bioavailability of CPI was significantly improved. These results have demonstrated that phytase treatment retained most of the original structure, and improved functional properties and digestibility of the protein isolate from Cinnamomum camphora seed kernel.