In order to study the relationship between the degree of deacetylation of chitin whiskers (CHWs) and their enzymatic degradation properties, in this paper, CHWs were first deacetylated to different degrees by alkali treatment, and the CHWs with the degrees of deacetylation of 17.84, 67.76, and 82.54% was obtained, respectively. Moreover, the partially deacetylated CHWs still maintained good crystallinity and nanoneedle-like morphology. Next, the in vitro degradation behavior of CHWs with different degrees of deacetylation was further studied under the single or synergistic action of lysozyme and lipase (37 °C, pH = 7.4). The results showed that the morphology change of CHWs was more obvious as the degree of deacetylation increased. The mass loss, the crystallinity index at the (110) crystal plane, and the concentration of reducing sugar of the CHWs also increased with the degree of deacetylation. Moreover, the synergistic effect of the two enzymes was more conducive to the degradation process of CHWs than single lysozyme or lipase. The difference in the rate of enzymatic degradation provides an idea for the regulation of the degradation rate of the CHWs.