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Enzyme activities play key roles in the biochemical functioning of soils, in processes such as soil organic matter formation and degradation, and nutrient cycling. They are indicators of soil quality and key to soil ecosystem functioning. In this study, the effect of vegetation communities and soil properties on the activities of invertase, alkaline phosphatase, amylase, urease, cellulose, and catalase were investigated in permafrost regions of the middle and western Qinghai-Tibetan Plateau. This area is characterized by cold, arid steppe, with an active layer thicker than 2 m. The results demonstrated that soil enzyme activities were higher in Stipa roborowskyi Roshev. vegetation communities than those of Carex moorcroftii Falconer ex Boott communities. Soil enzyme activities were lowest in the alpine cold desert area. The activities per unit soil were primarily positively related to soil organic C (SOC) and moisture contents, and when activities were expressed as per unit C, they were primarily positively related to gravel content and negatively to moisture content. Results demonstrated that the vegetation communities, SOC, and moisture contents were important factors influencing soil enzyme activities, while permafrost, vegetation cover, and topographic factors played less important roles in the cold, arid area of the northwestern part of Qinghai-Tibetan Plateau. Potential SOC changes in this area were also investigated with regard to future climate change.