Aiming to address the deficiency in mechanized harvesting equipment for cultivated bottle planting Lyophyllum decastes, an automated harvesting device was designed to achieve the transportation and positioning of the cultivation basket for bottle planting Lyophyllum decastes, the fixation of the cultivation bottle, low-loss and high-quality root cutting of Lyophyllum decastes, and flexible clamping and transportation. The overall structure and working principle of the device were explained. Through mechanical and kinematic analysis of the cultivation basket conveying process, the installation angle of the guide bar was determined to be 71°. Based on ANSYS LS-DYNA, a simulation analysis was conducted on the root cutting process. Considering cutting speed, feeding speed, saw blade rake angle, and tooth pitch as influencing factors, and the cutting force was used as the response index. The response surface method was used to analyze the significant impact of each factor on the index. The regression model was optimized and validated through bench tests. When the cutting speed was 6.49m/min, the feeding speed was 0.12m/min, the front angle was 25°, and the tooth pitch was 7mm, the cutting force was the smallest. A flexible finger for harvesting Lyophyllum decastes was designed. Based on the Yeoh model theory, the rubber material parameters were fitted by using uniaxial tensile testing. Single factor experiments were conducted by using ABAQUS software, and combined with actual experiments, the optimal bending performance was obtained. The structural parameters of the flexible finger were air cavity thickness of 2mm, 7 air cavities, air pressure at 25kPa, and a restricting layer thickness of 3mm. The overall machine trials demonstrated that the device operates smoothly, exhibiting excellent harvesting performance. The average net harvest rate, average loss rate, and average damage rate were recorded as 98.18%, 3.66%, and 2.75%, respectively. These results met the actual harvesting requirements for bottle planting Lyophyllum decastes, ensuring efficient and effective harvesting.