Using the theory and method of health economics,we analyzed CER and ICER in early elimination stage (2005-2009),the late elimination stage (2015-2010) and the post elimination phase (2016-).Results showed that annual total cost of investment was as following:64 235 144.8 Yuan in early elimination stage,11 250 248 Yuan in the late elimination stage,and 11 075 228.8 Yuan the post elimination phase.Effect analysis showed that the difference of the three-stage monitoring measures was statistically significant (P＜0.01).Number of cases within 3 days of onset (rate) prompt monitoring measures had the best effect in the late elimination stage,number of blood tests (rates),number of cases reported (rates) and number of cases within 1 days of onset (rate).Prompt monitoring measures had the best effect in the post elimination phase.CER and IC-ER showed that taking the number of blood test as the effect index,the monitoring measures in the late elimination stage were more cost effective.The number of cases reported,number of cases within 3 days of onset and number of cases within 1 day of onset were as the effect index,the monitoring measures in the post elimination phase were more cost effective.The elimination effect for monitoring measures after stage was optimal,cost the least,and might be the most effective.The study provides basic data for Fujian Province to strengthen the monitoring of imported cases of malaria on the construction of the management mechanism,and scientific and effective evaluation of monitoring measures,which has very important practical value and significance.