An embedded pneumatic picking-up mechanism was designed to solve the problem of complex structure and control instability existing in the traditional mechanical picking-up mechanism. According to the design requirements of picking-up mechanism, the constitution of mechanism, working principle and kinematics model of embedded pneumatic picking-up mechanism were clarified, and the control system based on singlechip was developed. The influence of mechanism parameter variation on the phase-trajectory of picking-up seedlings and the posture of picking-up arms were studied based on ADAMS software. The simulation results showed that the straightness deviation of picking-up trajectory was related to the length of lAD, lDE and l1, the height of picking-up trajectory was related to the length of lAD and lAC. The optimization combination of structural parameters achieved was as follows: lAD of 220mm, lAC of 170mm, lDE of 160mm and l1 of 313mm, while the height of picking-up trajectory was 130mm. When the height of picking-up trajectory was 80mm, the straightness deviation of picking-up trajectory was less than 2mm, the angle of declination was less than 4° at taking seedling stage，and the angle of declination was less than 1° at throwing seedling stage. The consistency verification experiment was carried out using high speed photography system. According to the seedling picking-up experiment, the success rate of seedling pick-up reached 93.0% and the success rate of dropping seedling attained to 89.5%, which satisfied the requirements of actual testing. The research for the automatic picking-up mechanism provided an important theoretical basis and reference for the design, analysis and further study on automatic picking-up and transplanting mechanism.