[Purpose/significance] This paper comparatively analyzes the associated features of Chinese and Japanese multi-scientific funds, and finds out the existing problems of Chinese multi-funds, to provide reference for standardizing the management decisions of multi-scientific funds.[Method/process] Choosing Chinese and Japanese funded scientific articles included by SCI in 2014 as the research object, it makes a comparative analysis on the associated distribution of two countries' scientific research funds, features of main cooperative networks and impact of main correlated funds with the method of social network analysis.[Result/conclusion] Among Chinese multi-funded scientific articles, 92.8% are mutually funded by national natural fund, national-state funds and local government's funds. 86.41% of Japanese multi-funded scientific papers are interrelated funded by funds of overseas, the Ministry of Education, JSPS, enterprises, JST and Ministry of Welfare.Compared with Japan, the sources of Chinese multi-scientific funds ate relatively single, so its development direction is to clarify the roles of various funds in science and technology system, reduce natural and governments' associated fund, and attract more mutual fund of overseas funds, enterprise funds and all kinds of social group funds.