In Korea, wide spread use of whole cottonseed, which is primarily a GMO plant imported from foreign countries and being fed to animals as raw state, has aroused concern that it may disturb the existing ecology of the country unless dispersion of the seed is under proper control. The objective of this study was to elucidate the changes in various nutritive parameters due to heat treatment and to determine the effective condition for removing germination ability of whole cottonseed (WCS). Of the various temperatures applied (76, 78, 80, 85, $100^{circ}C$/30 min) $85^{circ}C$ for 30 min was confirmed to be the lowest temperature treatment which resulted in a complete removal of the germination ability of WCS. Therefore, based on the determined temperature condition ($85^{circ}C$ 30 min) we tried to examine the changes of various nutritional parameters, including nutrient composition, in vitro digestibilities and ruminal protein degradabilities, comparing raw whole cotton seed (RWCS) and heated whole cotton seed (HWCS). Some changes in amino acid composition were observed with heat treatment of WCS, but these were regarded to originate from the variation in plant quality and seed morphology, which are usually affected by different environmental factors during the vegetation period. As for fatty acid composition, no significant differences were observed to occur during heat treatment. However, WCS heated at $85^{circ}C$ for 30 min in a circulating oven showed a significant decrease (p<0.05) of in situ rumen degradability in both dry matter (DM) and crude protein (CP), as compared to raw WCS. Overall results obtained in the study indicate that the heating condition used in this study, which was proven to be the most appropriate and economic to remove germination ability of WCS, may also improve the nutritional value of the ruminant with regard to reducing its protein degradability within the rumen.