This study explores the way to enhance research performance focusing basic and fundamental technology when researchers conduct international joint research with counterparts in foreign countries, funded under the National R&D programs. In order to retain validity and objectivity, mixed approaches including qualitative and quantitative are adapted at the first step. Through this step, main factors affecting the research performance can be addressed, such as the number of SCI papers published, conference attendance held both in domestic and foreign countries, researchers holding PhD involving in projects. Then, at the second step, DEA methodology is applied to explore the way to enhance research performance, based on the analysis at first step. The result at second step shows that the various ways can be drawn according to programs respectively and the general assumption of research funds and number of projects affecting positive outcome is not absolutely mentioned. Therefore, this study implies that input variables including research funds are not compatible with research performance in terms of international joint research and suggests further that the decisive outcome and management be reconsidered according to the programs respectively under the national R&D program.