The invention discloses a marine underwater detection bracket structure and an operation method thereof. The marine underwater detection bracket structure comprises a deck, a cabin, a crane, a vertical truss, detection equipment and a plurality of detection rods; the crane and the vertical truss are arranged on the deck; the deck is further provided with a plurality of rod storing rat holes and amounting rat hole within the hoisting range of the crane; the crane is equipped with a hoisting chuck; lifting tracks, a lifting device and a large hydraulic clamp are arranged on the vertical truss;the large hydraulic clamp is used for clamping the detection rods, the upper portion of the large hydraulic clamp is connected with the lifting device, and the rear side of the large hydraulic clamp is slidably connected to the lifting tracks through idler wheels; the mounting rat hole is located under the large hydraulic clamp; the detection rods can downwards penetrate through the mounting rat hole after being clamped by the large hydraulic clamp; and an operating platform is arranged in the cabin. The marine underwater detection bracket structure is easy and convenient to operate, and suitable for various water depths, and the detection stability can be improved by cooperating with the operation method.