The invention discloses a device and method for storing small boats. Cabins for storing the small boats are arranged on a boat body of the device, a channel which tilts downwards is formed in the stern portion of the boat body, one end of the channel is connected with the cabins, and a stern door which can rotate downwards is hinged to the other end of the channel. The stern door, the channel and the cabins are respectively provided with an idler roller set which is composed of a plurality of pairs of idler rollers supporting the bottoms of the small boats from the two sides. The two sides of the idler roller set on the cabins are respectively provided with a mobile guide rail, the mobile guide rail on each side is provided with a trolley, and each trolley is provided with a traction device and a boat pushing device. According to the device and method for storing the small boats, the stern door can be rotated downwards, the small boats can slide to the boat body from the idler roller set on the stern door through the channel, then the trolleys are used for pushing the small boats to the corresponding positions of the small boats to be fixed, operation is convenient, the purpose that the storing device in one mother boat can be used for storing a plurality of small boats, operation is convenient, and the safety is high.