Abstract: 242 Taiwan-related research projects which were supported by Fujian Provincial Department of Science and Technology since 1987 are statistically analyzed. The results showed that the amount of Taiwan-related research projects in Fujian had been yearly increased since 2005, peaked during 2008-2011, taking 50.4% of the total. Within all research projects when divided by research types, the soft science got the maximum rate of 50.8%. The ratio of projects in agriculture was 56%. And the largest proportion of top two in Taiwan-realted research projects undertook by Fujian Academy of Agricultural Sciences and Fujian Agriculture and Forestry University undertook were 14.9% and 8.7% respectively. In addition, several strategies were proposed to strengthen the cross-strait project establishment and subsidization.