Evapotranspiration is essential for precise irrigation and water resource management. Previous literature suggested that eddy covariance (EC) systems could directly measure evapotranspiration in agricultural fields. However, the eddy covariance method remains difficult for routine use, due to its high cost, operational complexity, and relatively multifaceted raw data processing. An alternative method is the flux variance (FV) method, which can estimate the sensible heat flux using high-frequency air temperature measurements by fine-wire thermocouples, at relatively low-cost and with less complexity. Additional measurements of the net radiation and soil heat flux permit the extraction of latent heat flux through the energy balance closure equation. This study examined the performance of the FV method and the results were compared against direct eddy covariance measurements. Data were collected from September 2020 to August 2021, covering seasonal variations. Due to the method’s limitation, only the data under unstable conditions were used for the analysis and days with rainfall were omitted. The results showed that the FV-estimated sensible heat flux was in good agreement with that of eddy covariance in the seasons of winter 2020 and summer 2021. The best agreement between the estimated and measured sensible heat fluxes was observed in the summer, with R2 = 0.83, RMSE = 34.97 Wm−2 and RE = 8.20%. The FV extracted latent heat flux was in good agreement with that measured by EC for both seasons. The best result was obtained in the summer, with R2 = 0.92, RMSE = 23.12 Wm−2, and RE = 6.37%. Overall estimations of sensible and latent heat fluxes by the FV method were in close relation with the eddy covariance data.