In the biofuel supply chain, there may be various and hybrid uncertainties that, if ignored, can lead to inefficient network design. In this study, a multi-objective robust fuzzy stochastic programming (MORFSP) model is proposed for designing biodiesel supply chain network (BSCN) under different and hybrid uncertainties. This model simultaneously minimizes total cost of the BSCN and total environmental impacts of activities of the network. Fixed costs and environmental impact of opening facilities are described as fuzzy variables. Demands, supplies, other costs and environmental impacts are considered as fuzzy scenario based variables. The proposed MORFSP model considers different risks, including possibilistic variability and scenario variability related to economic and environmental objective functions, and unsatisfied demand costs. This model is applied in a real case study to design a BSCN in Iran. Waste cooking oil (WCO), and some non-edible plants like Salvia lerifolia (SL) and Jatropha Curcas L. (JCL) are considered as sources of producing biodiesel. The proposed approach used for designing a four-echelon, multi-period, and multi-product, of BSCN. The results show the effectiveness of the proposed model for designing the BSCN under hybrid uncertainties.