In the nursery factory for rice potseedlings, the soft plastic potseedling tray is embedded into a hard tray manually which increased the cost and the labor intensity. In order to improve the automation level of rice pot seedling nursery factory, an automatic soft tray separating and embedding machine was designed, which can be integrated with the rice seeding pipeline to reduce the cost and improve the efficiency. The automatic soft tray separating and embedding machine mainly consisted of tray separating section and tray embedding section. The separating section included the vacuum clamping mechanism and tray lifting mechanism;the embedding section included the tray turnover mechanism, embedding mechanism and conveying mechanism. According to the pulling force test for separating soft tray, the peak tensile force was varied in the range of 0.807~2.030N. The vacuum suckers were used to separate the plastic soft trays that were stacked upside down. Then the type and amount of the vacuum suckers was determined. The catching points were set at the outer wall of the holes on the edge of the tray which had enough space for the suckers. By analyzing the overall force applied to the tray, the minimum air pressure for separating the tray was calculated to be 57.924kPa. After the tray was separated, it was turned 180°by the tray turnover mechanism and sent to the tray embedding section. A hard tray was conveyed and stopped at a fixed position by the conveying mechanism.Then the tray embedding mechanism clamped the tray and moved downward to place the soft tray into the hard tray. The kinematic analysis of the separation mechanism was carried out. The open width variation of the clamping mechanism was determined, so that the time required for the clamping mechanism to clamp the tray can be calculated. The minimum separation height of 20.47mm was determined based on the tray deformation analysis by ANSYS, the height of the tray and the gap between the trays. According to the design requirements of the overall machine, the control scheme of the system was designed, including the control of the solenoid valve in the air pressure loop and the control of the motor in the mechanism. The overall machine was modeled by using SolidWorks. Based on the machine model, the prototype was manufactured, and the experiments of separating and embedding tray were carried out. 220V single-phase alternative current was used to power the air compressor and the prototype respectively. The pressure regulating valve of the main pneumatic circuit was set to be 0.45MPa. The experiments were conducted on 14×29 hole trays with clean surface and some water and soil adhered on the surface respectively. The results showed that by using eight 6mm vacuum suckers, the success rate of separating and embedding 14×29 hole clean seedling tray was 97%. In the case of water and soil adhered on the surface of the tray, the success rate of separating and embedding 14×29 hole seedling tray was 98%. The machine efficiency was 435 trays/h, which could meet the working requirements of the factory seeding line.