Due to the dual hydrological structure and the high heterogeneous habitat in the Karst region of southwest China, the water and heat processes at land surface are very complicated. The weakness of research on the mechanisms of water movement and heat transfer among soil, vegetation and atmosphere has become the key hindering factor for identifying the mechanism of ecosystem degradation and promoting ecosystem restoration and reconstruction. In this paper, we firstly summarized three methods for investigating water and heat processes in Soil-Plant-Atmosphere Continuum (SPAC): Field observation and experiments, parameterization of land surface processes and remote sensing technology. It was pointed out that with respect to this kind of study in the southwestern karst region, the systematic observation and experiments at the scales of sample plot and slope are necessary and urgent, which is helpful for deepening the mechanism research on water and heat processes in SPAC and further promoting the development of karst-region-suitable land surface and remote sensing model. And then, we discussed the progresses in the research of water and energy balance at land surface in the southwestern karst areas: emphasizing the study on water cycle, but neglecting the research on energy balance and water-heat coupling. Due to the special geological background and highly heterogeneous habitat, the mechanisms for spatial variability of soil moisture, slope rainfall infiltration and runoff generation were not fully understood. Finally, we explored the prospects of studies on water and energy balance in this region from three aspects: The mechanism of water and energy processes, the influencing mechanism for differences in water and energy processes between different stages of karst rocky desertification, and the regulation of ecological restoration and reconstruction based on the viewpoint of water and heat balance. This study could be helpful for developing studies on rocky desertification containment and ecosystem rehabilitation.