A Multi-input single inductor dual-output Boost based architecture for Multi-junction PV energy harvesting source is presented. The system works in Discontinuous Conduction Mode to achieve the independent input regulation for multi-junction PV source. A dual-output path is implemented to regulate the output at 3V as well as store the extra energy at light load condition. The dual-loop based sliding-mode MPPT for multi-junction PV is proposed to speed up the system response time for prompt irradiation change as well as maximize MPPT efficiency. The whole system achieves peak efficiency of 83% and MPPT efficiency of 95%. The whole system is designed, simulated in Cadence and implemented in PCB platform.