A navigation system includes: a control unit configured to calculate a non-terrestrial navigation route for guiding a multimodal vehicle during a non-terrestrial travel segment; calculate a ground navigation route for guiding the multimodal vehicle during a ground travel segment beyond a mode-transition point; generate a composite navigation route based on the non-terrestrial navigation route and the ground navigation route for continuously guiding the multimodal vehicle over the non-terrestrial travel segment and the ground travel segment; and an interface unit, coupled to the control unit, configured to communicate the composite navigation route.