The invention relates to a bidirectional continuous underway seismic refraction method observation system applicable to complex water area exploration. The bidirectional continuous underway seismic refraction method includes the following steps that first, preparatory work is done; second, underway exploration is carried out, and time parameters T and coordinate parameters S in both directions are acquired; third, reciprocal reverse control hodographs are drawn; fourth, the focal depth H can be obtained through formula calculation, and seismic refraction exploration in a complex water area is interpreted. According to the bidirectional continuous underway observation system, for the two banks, a single hodograph is continuously chased from one bank to the opposite bank, chasing observation is repeated, and a reciprocal shot point is determined through sound velocity in water so as to achieve the encountering purpose; then, on the basis of the equality in the interchange of seismic refraction waves and the parallelism principle of refraction wave hodographs, seismic refraction exploration in complex water areas such as a water surface is achieved, the exploration process is simplified, the exploration accuracy is improved, it is guaranteed that the design of tunnels and the like is reasonable, scientific and safe, and gaps in the field of complex water area exploration at home and aboard are filled in.