The invention discloses a micro-lysimeter soil sample collecting method which is designed in order to reducing the damage on a soil sample original state. The micro-lysimeter soil sample collecting method comprises the steps of adopting the same original point as a circular center, and drawing a collecting circle adopting a first diameter as the diameter, and a hole digging circle adopting a second diameter as the diameter in a soil sample collecting area center; on the sample collecting circle, adopting a soil sample collecting cutter to insert into a lower soil layer, separating a cylindrical soil sample to be collected from soil around the soil sample, digging and removing a half of soil at an annular structure part between the collecting circle and the hole digging circle, and forminga notch under the cylinder to be collected; jacking the cylindrical soil sample to be collected, and bringing back to a sample plot for carrying out a soil lysimeter experiment. According to the micro-lysimeter soil sample collecting method provided by the invention, the occurrence of the phenomenon that a soil sample is too big or too small or a shape drawing does not conform to the requirement of a micro-lysimeter on the soil sample after a soil sample is collected through a traditional method is avoided, and the workload of follow-up processing after the soil sample is collected is reducedto a large extent.