The invention discloses a combined foundation structure suitable for a lagoon face island-reef environment and a construction method thereof, and relates to the field of geotechnical designs and island-reef development. The combined foundation structure suitable for the lagoon face island-reef environment and the construction method thereof are suitable for coral lagoon geological conditions. The combined foundation structure suitable for the lagoon face island-reef environment comprises high-pressure jet grouting stabilization piles, a prefabricated caisson, lateral restraining high-pressure jet grouting piles, prefabricated bored sinking pipe piles and a prefabricated bearing platform, wherein the prefabricated caisson is located on the high-pressure jet grouting stabilization piles and in a curtain structure formed by the lateral restraining high-pressure jet grouting piles and is in rigid connection with the prefabricated bearing platform into a whole for collaborative bearing through the prefabricated bored sinking pipe piles. The combined foundation structure suitable for the lagoon face island-reef environment and the construction method thereof not only overcome the disadvantageous engineering characteristics of a coral lagoon foundation structure such as high structural performance, low bearing capacity and large deformation, but also bring the bearing capacity of each layer of rock and earth mass of the coral lagoon foundation structure into full play, have the characteristics of large rigidity, high bearing capacity and fast, excellent and economical construction and the like, have the advantage of adapting to construction in island areas, have broad application prospects, and make it possible to build an airport and other overhead reclamation engineering on a coral lagoon foundation.