Forest gap is a common form of disturbance in forest ecosystems. Exploring the effect of flooding on the spatial and temporal heterogeneity of the microenvironment within forest gaps is important to reveal the changes of species diversity and their renewal characteristics in desert riparian forests. In this study, a sample plot of forest gaps of similar size was selected in each of the non-flooded areas and flooded areas in the middle reaches of the Tarim River. The air temperature and humidity in different directions within the forest gaps were monitored using a portable meteorological monitor. The spatial and temporal distribution differences of the microenvironment within the forest gaps under different flooding conditions were compared and analyzed to lay the foundation for an in-depth exploration of the vegetation regeneration mechanism of desert riparian forests. The results showed that:(1) the air temperature in the forest gaps of both non-flooded and flooded areas presented a trend which increases at first and then decreases; the air humidity showed an opposite trend which decreases at first and then increases. There was an obviously negative correlation between temperature and humidity in the same sample plot, while the flooding changed the forest microenvironment, increasing humidity and lowering the temperature in the forest gaps. (2) The difference in temperature distribution between the non-flooded areas and the flooded areas of the forest gaps in different directions was small, and the flooded areas had little effect on the temperature change. The process of humidity change within the forest gaps of the two sample sites was more complicated and the difference was obvious, and the gradient of humidity change was more intensive in the flooded areas. (3) The temperature difference boundaries between the non-flooded and flooded areas were obvious. The temperature difference was smaller in the south-west direction and the largest in the center. Flooding did not change the temperature trend in different directions. The humidity gap was larger in the north of the center, with the non-flooded areas having a smaller humidity gap in the northwest, while the smallest humidity gap in the flooded areas appeared in the southwest. The results show that the spatial and temporal variation in the microenvironment of forest gaps in desert riparian forests is specific to arid zones, and also elucidate the responses of forest gap microenvironments to flooding. This provides a scientific basis for an in-depth study of forest gap disturbance on the renewal and succession of desert riparian forests.