In this paper, using MATLAB SIMULINK, a generalized design methodology was suggested for multi pass transmission(MPT) by classifying the vehicle power train as prime mover, MPT and vehicle dynamics. This approach enables a designer to investigate the influence of each transmission component by simple combination of system components without changes of overall program. Using the design methodology, a MPT consisting of CVT, 2, clutches and reduction gears was designed for a braking energy regenerative flywheel hybrid vehicle. The CVT is essential in order to connect the engine and flywheel speed with the vehicle speed. For the purpose of smooth clutch operation, control algorithm was suggested by introducing dead zone for the clutch engagement. Using the SIMULINK model, performance of the flywheel hybrid vehicle with MPT was investigated. It was observed from the simulation results that the MPT vehicle showed better fuel economy, 47% than that of AT vehicle, 27% than that of CVT vehicle for ECE-15 driving cycle. Especially destinct fuel efficiency improvement was obtained for city driving cycle requiring more frequent stop and start.