As an internationally recognized standard method for carbon flux determination, the eddy covariance method has a broad space in the field of agro-ecosystem carbon flux studies. To provide references for eddy covariance method and carbon flux research in agro-ecosystem, the study aims to summarize the latest research results of agro-ecosystem carbon flux based on eddy covariance method. This paper reviews the research status of carbon flux over agro-ecosystem based on the eddy covariance method at home and abroad, and also put emphasis on the latest research results on the temporal variation characteristics, driving factors, productivity models and data processing. Through literature research, it is found that the eddy covariance method has many researches on the temporal variation characteristics of carbon flux in agro-ecosystems, and many research results show that the daily and seasonal changes of farmland carbon flux show a single-peak “U” trend in single planting mode, while in the multi-crop planting mode, the seasonal change is “W” type. But the carbon flux research on planting mode lacks regional representation. At the same time, the driving factor research focuses on the influence of environmental factors such as temperature, light and moisture on farmland carbon flux. Less research on the relationship between environmental factors and agronomic measures was done. And there is a lack of uniform standards for the processing of flux night data and elimination or interpolation of the invalidation and missing data. Therefore, this paper points out that the long-term continuous monitoring at the typical planting mode, multi-factor collaborative analysis, data quality control should be the important research directions.