Abstract: Based on the SCI-E database, the published papers in Fujian and Taiwan from 2005 to 2014 were statistically analyzed. The results showed that: ①the total amounts of the published papers in the ten years of Fujian and Taiwan were respectively 35204 and 199733, and the annual growth rate of Fujian was much higher than that of Taiwan. ②English was the main language used in the published SCI papers of Fujian and Taiwan, and the ratios were respectively up to 95.02% and 99.94%. ③The research article was the main documental type, and the ratios were respectively up to 94.46% and 87.69%. ④Chemistry, material science, physics, engineering and mathematics were the top five dominant disciplines of Fujian, whose ratio was up to 71.91%; while engineering, physics, chemistry, material science and computer science were the top five dominant disciplines of Taiwan, whose ratio was up to 61.27%. ⑤The source publications of Fujian’s and Taiwan’s SCI papers were not highly centralized, and the ratios of the top source publication were respectively only 1.56% and 1.14%. ⑥The universities were the main institution that published SCI papers in Fujian and Taiwan, and the ratios were both up to 80%. ⑦The published SCI papers of Fujian and Taiwan were mostly funded by the National Natural Science Foundation and Taiwan scientific council respectively. ⑧The most important country which Fujian and Taiwan collaborated the SCI papers with was both America, and the ratios were respectively up to 9.74% and 11.99%. ⑨The paper amounts of Fujian and Taiwan that published in the top journals were respectively 36 and 359.