To address the issues of poor positioning accuracy, low supply efficiency and inadequate adaptability for different tray specifications of the existing seedling tray conveying device, a dual-axis positioning tray conveying device was developed, which can accommodate seedling trays ranging from 21 to 288 holes. A dual-sensor positioning algorithm and variable displacement positioning method were proposed to increase the efficiency, ensuring precise initial positioning and intermittent movements both along the seedling conveyance (X-axis) and platform movement (Y-axis). The system utilizes a precise positioning servo-control system with three-closed-loop controls and a PID algorithm enhanced through simulation to refine seedling positioning accuracy. Experiments with nine different tray specifications were conducted on a step-controlled platform to test suitability, validating the performance of the initial positioning and intermittent transport in both the X and Y directions. On the X-axis, the initial positioning deviation of the seedling tray was up to 1.34 mm and the maximum deviation in the intermission conveying was 0.85 mm. Comparatively, the deviation on the Y-axis was smaller, with the initial positioning deviation up to 0.99 mm and the intermission moving deviation up to 0.98 mm. These results demonstrate that the designed device meets the requirements for precise transport, providing essential technological foundations for seedling tray transport and retrieval steps in fully automated transplanting machines.