The invention relates to a flexible ship body connecting mechanism of a combined type semi-submerged ship. The flexible ship body connecting mechanism is characterized in that a ship body connecting direction is set as an X axis and a horizontal direction perpendicular to the ship body connecting direction is set as a Y axis; a joint part of two adjacent ship bodies is divided into a first unit body and a second unit body; a plurality of bearing bases (3) are arranged in the Y direction of the first unit body; tapered pins (2) which are in corresponding fit with the bearing bases (3) are arranged on the second unit body, and each tapered pin (2) is driven by a respective hydraulic oil cylinder (1) to be inserted into or pulled away from the corresponding bearing base (3) in the Y direction, so that the connection and the separation of the ship bodies are realized; the first unit body and the second unit body can oppositely rotate around the tapered pins (2); hydraulic oil cavities (4) with buffer springs (4) therein are arranged on the upper and the lower parts of the first unit body or the second unit body; when the two unit bodies are connected, contact buffer is firstly performed through the hydraulic oil cavities (4), and then the tapered pins (2) are driven to be in locking connection through the hydraulic oil cylinders (1).