The invention discloses a hydraulic system for a stratum sampling instrument. The hydraulic system comprises an oil tank, a filter net, a high-speed plunger pump, a high-speed motor for driving the high-speed plunger pump, a balancing oil bag, a boosting oil cylinder, a sucking oil cylinder, two packing oil cylinders, four solenoid reversing valves and seven check valves. According to the hydraulic system for the stratum sampling instrument, the high-speed motor is adopted to be matched with the high-speed plunger pump, a large flow is output in a small structure and volume range, the hydraulic system has all packing and sucking functions of the hydraulic system of the existing stratum sampler, a system oil path is integrated by combining with selection and optimization of a hydraulic element, the hydraulic element adopts the high-speed plunger pump special for aviation instead of a duplex gear pump, the hydraulic loop is simplified, the number of elements is reduced, and the hydraulic system has the characteristic of efficiency and energy saving.