This paper presents a multi-criteria decision-making method based on Vague sets to evaluate the eleven main competitive research funding programs of the National Natural Science Foundation of China (NSFC)．Firstly，panels of NSFC were asked to evaluate these funding programsby a questionnaire according to four criteria: assessment fairness，management normalization，scientific innovation，and social influence．Three linguistic terms，“HIGH”，“LOW”or“UNKNOWN”，are involved in the evaluation． Secondly，the linguistic evaluations associated with each funding program were translated into Vague evaluations，and the evaluation scores of each program according to each criterion were measured using anovel scoring function proposed in this paper． Finally，the normal distribution-based OWA operator was applied to aggregate the evaluation scores according to each criterion，and aggregated scores of each programwere attained． The conclusion in this paper can provide an important decision support for improving the support structure and management mode of NSFC．