The promotion of clean energy in ecologically fragile areas in Northwest China is imminent, and income is an important factor in rural energy consumption. Based on the data of 969 rural households, the binary logistic model is used to analyze the impact of income level on clean energy use behavior of rural households in ecologically fragile areas in Northwest China, and its heterogeneity. The results reveal that there are differences and spatial heterogeneity in the impact of income level on rural household clean energy use behavior of different types of use in ecologically fragile areas in Northwest China. With the increase of income level, in ecologically fragile area on Loess Plateau, where the proportion of clean heating is far lower than that of other types of use, the probability of clean heating increases the most. In ecologically fragile area on desert areas in Northwest China, where the utilization rate of clean energy for various types of use is high and the difference is small, the probability of cooking with low cost increases the most. However, in ecologically fragile area on Qinghai Tibet Plateau, where clean energy utilization rate is the lowest and high-income herdsmen are the majority, the impact of income levels in three types of uses is not significant. Based on this, it provides policy reference for the rural energy transformation in ecologically fragile areas in Northwest China.