A vapour compression system (1) comprising at least two evaporator groups (5a, 5b, 5c), each evaporator group (5a, 5b, 5c) comprising an ejector unit (7a, 7b, 7c), at least one evaporator (9a, 9b, 9c) and a flow control device (8a, 8b, 8c) controlling a flow of refrigerant to the at least one evaporator (9a, 9b, 9c). For each evaporator group (5a, 5b, 5c) the outlet of the evaporator (9a, 9b, 9c) is connected to a secondary inlet (12a, 12b, 12c) of the corresponding ejector unit (7a, 7b, 7c). The vapour compression system (1) can be controlled in an energy efficient and stable manner. A method for controlling the vapour compression system (1) is also disclosed.