Since the introduction of assembly lines, they are being used for the mass production. Due to the concept of mass customization, Mixed-Model Assembly Lines (MMAL) are becoming more popular. Various Industries are forced to shift to MMAL because of customer demand of more customized products. Assembly line balancing and model sequencing are the two major problems in MMAL. This paper deals with the Model sequencing problem in MMAL. A modified Multi-Objective NEH (MO-NEH) algorithm was proposed to optimize the conflicting objectives (flow time and make-span). For this purpose, NEH was integrated with PROMTHEE-II, a Multi-Criteria Decision-Making technique (MCDM). A mathematical model was presented for three Objectives; make-span, Idle time and flow time. A case study of hydraulic pumps MMAL was conducted. Results of proposed MO-NEH was compared with existing NEH variants and it showed that proposed algorithm outperformed the existing variants in optimizing the objectives simultaneously.