The high‐humidity mountain forest ecosystem (HHMF) of Jinyun Mountain in Chongqing is a fragile ecosystem that is sensitive to climate change and human activities. Because it is shrouded in fog year‐round, illumination in the area is seriously insufficient. However, the flux (energy, wa-ter) exchanges (FEs) in this ecosystem and their influencing factors are not clear. Using one‐year data from flux towers with a double‐layer (25 m and 35 m) eddy covariance (EC) observation sys-tem, we proved the applicability of the EC method on rough underlying surfaces, quantified the FEs of HHMFs, and found that part of the fog might also be observed by the EC method. The observation time was separated from day and night, and then the environmental control of the FEs was determined by stepwise regression analysis. Through the water balance, it was proven that the negative value of evapotranspiration (ETN), which represented the water vapor input from the atmosphere to the ecosystem, could not be ignored and provided a new idea for the possible causes of the evaporation paradox. The results showed that the annual average daily sensible heat flux (H) and latent heat flux (LE) ranged from −126.56 to 131.27 W m−2 and from −106.7 to 222.27 W m−2, respectively. The annual evapotranspiration (ET), positive evapotranspiration (ETP), and negative evapotranspi-ration (ETN) values were 389.31, 1387.76, and −998.45 mm, respectively. The energy closure rate of the EC method in the ecosystems was 84%. Fog was the ETN observed by the EC method and an important water source of the HHMF. Therefore, the study area was divided into subtropical mountain cloud forests (STMCFs). Stepwise regression analysis showed that the H and LE during the day were mainly determined by radiation (Rn) and temperature (Tair), indicating that the energy of the ecosystem was limited, and future climate warming may enhance the FEs of the ecosystem. Addi-tionally, ETN was controlled by wind speed (WS) in the whole period, and WS was mainly affected by altitude and temperature differences within the city. Therefore, fog is more likely to occur in the mountains near heat island cities in tropical and subtropical regions. This study emphasizes that fog, as an important water source, is easily ignored in most EC methods and that there will be a large amount of fog in ecosystems affected by future climate warming, which can explain the evaporation paradox. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.