The purpose of this study was to chemically modify the surface of chitin whiskers and to investigate the effect of the incorporation of these modified whiskers into a natural rubber (NR) matrix on the properties of the ensuing nanocomposite. Different chemical coupling agents were tested, namely, phenyl isocyanate (PI), alkenyl succinic anhydride (ASA) (Accosize 18 from American Cyanamid), and 3-isopropenyl-alpha,alpha'-dimethylbenzyl isocyanate (TMI). The extent of chemical modification was evaluated by Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), and surface energy analysis. After chemical modification, nanocomposite films were obtained using a toluene natural rubber solution in which the whiskers were dispersed. Their mechanical properties were found to be inferior to those of unmodified chitin/NR composites presented in our previous study. In fact, even though there is an increase in filler-matrix interaction as a result of chemical modification of the chitin whiskers, this does not contribute to the improvement in the mechanical properties of the resulting nanocomposite. It is concluded that this loss of performance is due to the partial destruction of the three-dimensional network of chitin whiskers assumed to be present in the unmodified composites.