The application provides a deep-water shallow geological disaster simulation system, comprising: a pre-selected outdoor experimental site provided with a first simulation formation, a shallow-gas-containing simulated formation, a sand-bearing simulated formulation, a shallow-flow-containing simulated formation and a second simulated formation in sequence; a signal transmitter arranged at one end of the pre-selected outdoor experimental site close to the second simulated formation; a signal receiver arranged at the end of the pre-selected outdoor experimental site close to the first simulated formation; a signal transmission and receiving control system; a first embedded injection pipeline having one end positioned in the shallow-flow-containing simulated formation and the other end connected to a boost pump; a second embedded injection pipeline having one end positioned in the shallow-gas-containing simulated formation and the other connected to a boost gas pump. A compact mud seal-up unit is arranged between the shallow-gas-containing simulated formation and the shallow-flow-containing simulated formation. By using the deep-water shallow geological disaster simulation system provided by the embodiment of the invention, it is possible to improve fitness between the simulated deep-water shallow geological disaster simulation system and an actual deep-water sallow geological disaster.