The invention discloses a deep-water soft soil foundation quay wall type wharf structure and a construction method thereof, comprising a reinforced soft soil foundation, a foundation bed before riprap, a foundation bed after riprap, a front caisson, a rear caisson, a riprap slope embankment, The front parapet, rear parapet, beam-slab structure and backfilling of the wall; the end of the reinforced soft soil foundation near the deep water is provided with a pre-riprap bed; The front breast wall; the back of the riprap front bed is provided with a riprap rear bedding, the top of the riprap post bedding is provided with a rear caisson, the top of the rear caisson is provided with a rear breast wall, and the rear of the rear caisson is provided with wall backfill; A riprap slope embankment is set between the front caisson and the rear caisson, and a beam-slab structure is set between the front parapet and the rear parapet; the invention can directly build a bank-type wharf on the deep-water soft soil foundation, and has both the functions of a wharf and a dike , not only can save the trestle bridge, but also can greatly increase the land use area, which has high value.