Background Malaria is an insect-borne infectious disease that spreads through bites from infected Anopheles mosquitos. The disease seriously endangers human health and economic development. Against the background of eliminating malaria in Fujian Province, in order to understand the cost and benefit of malaria monitoring measures, the health economics of the monitoring measures should be examined..Methods The malaria epidemic data during the malaria elimination stage (2005–2019) in Fujian Province were collected and sorted. The basic economic data were obtained from the Fujian Statistical Yearbook. A cost-benefit analysis was conducted for this study, based on the fundamental theories in health economics. Moreover, the Cost (C) of monitoring measure during the malaria elimination stage was calculated, and the Benefit of malaria elimination stage (B) was analyzed.Results The total cost of monitoring measures in the malaria elimination stage was about 607,878,783.36 yuan ( USD $ 87,534,544.80). The proportions of the costs were as follows: case detection and treatment was 66.62%, health education was 13.31%, epidemic monitoring was 10.05%, supervision and assessment was 5.15%, and training and meeting was 4.87%. The total benefit of the malaria elimination stage was about 116,123,417,911.81 yuan (USD$ 16,721,772,179.30), the economic benefit was 22.61%, and the social benefit was 77.39%. The cost-benefit analysis of the malaria elimination stage showed that the NB of monitoring measures was about 115,515,539,128.45 yuan (USD$ 16,634,237,634.50) and the BCR was 191.03. The monitoring cost for residents was 1.08 yuan (USD$ 0.16) per capita, and the benefit for residents was 206.12 yuan (USD$ 29.68) per capita. Conclusion In the past 15 years, malaria control work has achieved excellent economic and social benefits in Fujian, China. The work should continue in strengthening the monitoring and control of imported malaria cases, increasing health education in high-risk locations (such as those frequented by entry-exit personnel), and enhancing residents’ awareness about prevention and personal protection. The work should continue to be consolidated for the elimination of malaria. The framework and results of this study conform to the principles of health economics and have a certain reference value for current malaria monitoring practices.