A daily-scale flux variance (FV) method, which employs low-frequency air temperature measurements, was assessed against eddy covariance (EC) measurements of sensible and latent heat fluxes at four sites representing grassland and cropland ecosystems. The sensible heat flux was estimated using two daily-scale FV approaches: M1 (separating daytime and nighttime data) and M2 (integrating daily data), both derived from conventional formulations. The latent heat flux was extracted as a residual of the energy balance closure with the FV-estimated sensible heat flux and additional measurements of net radiation and soil heat flux. The results showed that the FV method performed poorly in estimating sensible heat flux across all four sites, primarily due to the negative flux values from cropland sites. In contrast, latent heat flux estimation showed reasonable agreement with EC measurements. Notably, upscaling the FV method from a half-daily (M1) to a daily (M2) scale did not improve the accuracy of sensible and latent heat flux estimations for most sites. The best performance for latent heat flux was achieved with M1 at a cropland site (YF), yielding a slope of 0.98, determination coefficient of 0.88, and root mean square error of 13.13 W m⁻². Overall, the daily-scale FV method—requiring only low-frequency air temperature data from microclimate systems—offers a promising approach for evapotranspiration monitoring, particularly at basic meteorological stations lacking high-frequency instrumentations.