Scheduling of wind-photovoltaic-hydropower systems is a complex multi-objective collaborative problem which requires multi-criteria decision making (MCDM) to assist in formulating the most-preferred scheduling scheme. There are uncertainties existing in criteria weights (CWs) due to the limitations of the knowledge level of decision makers and the subjectivity of preferences. This paper proposes a two-stage stochastic multi-criteria group decision making model considering the uncertainties in the decision making environment and the progression of the decision making process. For the prophase decision making (the first stage), the stochastic multi-criteria acceptability analysis (SMAA) theory and the MCDM model VIKOR are combined to construct a SMAA-VIKOR model for inverse weight space analysis on the situation that the initial CW information is completely unknown. In the second stage of decision making, the decision makers are allowed to express their fuzzy preferences based on the information provided in the first stage by coupling the intuitionistic fuzzy analytic hierarchy process (IFAHP) into the SMAA-VIKOR model to obtain the final scheme. The wind-photovoltaic-hydropower system in Yalong River Basin is selected as the case study. Results show that among the 12 alternative schemes, scheme A2 is ranked first with the probability of 0.69 in the first stage while the probability of taking the first ranking in the second stage is increased to 1. More explicit ranking results are obtained based on the results of the first stage, which effectively enhances the confidence of decision makers and improves decision making efficiency.