A hybrid electronic design system and a reconfigurable connection matrix thereof are disclosed. The electronic design system includes a virtual unit, a hybrid unit and a communication channel. The virtual unit further includes a plurality of proxy units, a plurality of virtual components and a driver. The virtual components are connected with the driver via the proxy units. The hybrid unit further includes an emulate unit, a physical unit and a chip level transactor. The chip level transactor is connected with the emulate unit and the physical unit. The communication channel is connected with the driver of the virtual unit and the chip level transactor of the hybrid unit.