The invention discloses a method and device for acquiring the deposition layer section of a hydraulic test tank. The method comprises: after finishing a hydraulic deposition test, using a liquid nitrogen freezing method to freeze a section to be tested, and freezing the water and underwater deposit of the section to be tested into ice cubes together so as to solidify the sample, and then taking out the solidified section sample. The device for realizing the method is composed of a water tank, separation boards, an inner cooling pipe, an outer cooling pipe, a thermal insulation layer, and a liquid nitrogen bottle. Two separation boards are respectively disposed at the upstream and downstream of the sample section. The inner cooling pipe and the outer cooling pipe are respectively positioned inside and outside the water tank. Suspended at the mouth of the water tank, the inner cooling pipe is about 20-40mm from the sidewalls and the bottom deposition layer surface of the water tank, while the outer cooling pipe is close to the outer walls of the water tank. The method and device of the invention solves the difficult problems of accurate sampling and measuring in experimental research of the deposition, transfer and conversion rules of silt, organic matters, heavy metals and other pollutants in rivers, lakes and oceans, thus being suitable for research of multilayer deposits.