Allium chinese is one type of the small underground bulb crops, mainly distributed among the hilly and mountainous areas in southern China. The growing place is normally characterized by the complex and changeable terrain with the high soil viscosity. Therefore, some difficulties can be posed as the mechanized harvesting of Allium chinense, such as the high requirements for separating fruit and soil, the great difficulty in separating, and terrain adaptability. In this study, a fruit soil separation technology was developed for the "rod and sieve type vibration separation + roller pushing type multistage separation". A walking device with high chassis crawler was adopted to place the working parts, such as the adjustable digging device, the rod and sieve type vibration separation device, and the roller pushing types multistage separation device between the two crawlers. The size of the machine was reduced suitable for the small plot harvesting operation under complex terrain. The excellent working performance was achieved in the digging shovel in the middle of the crawler. The strong stability of excavation depth was promoted in the fruit-soil separation of the less excavation depth. The rod and sieve type vibration separation device was realized the first step of conveying and separation by vibrating and impacting the clods. There were different linear speeds at the root and end of the vibrating rod. Specifically, the large clods were used to turn over the clods, and then cause the clods to be longitudinally sheared and damaged. Excellent conditions were created for the subsequent separation of fruit and soil. The clod was crushed and fell back to the field, as the fruit holding space was changed to form the adjacent rollers during the operation of the Roller pushing type multistage separation device. The fixed soil pressure rod of soil crushing was used to squeeze the clods into the fruit holding space, in order to achieve the efficient crushing of the soil block for the better fruit and soil separation. As such, the large clods were avoided to transport on the surface of the roller group without entering the fruit holding space. Each device in the working process was analyzed using theoretical calculation and simulation. The key parameters were obtained, such as the position and depth of the adjustable digging device, the amplitude and crank speed of the rod and sieve type vibration device, as well as the size and position of the roller. The Allium chinense harvester was finally developed, including the adjustable digging, the rod and sieve type vibration, and the roller pushing type multistage separation device. The field excavation test were designed to verify the performance of each device and the complete machine. It was found that there was the stable actual digging depth of the machine, where the rate of missed digging was 0.31%, the rate of buried fruit was 3.20%, the total rate of damaged fruit was 5.87%, and the effective harvest rate was 93.23%. Therefore, the stable performance was achieved in the reasonable structure design and layout of the whole machine. The improved harvester can fully meet the demand for the mechanized harvesting of Allium chinense under the current hilly and mountainous conditions.