HighlightsThe spatial four-bar linkage mechanism is applied to the apple orchard seedling-lifting machines.The dimension synthesis of spatial four-bar mechanism is applied to the design of agricultural machinery.A new type of soil cleaning device for apple orchard seedling-lifting machines was designed.Compared with the traditional soil cleaning device, the new soil cleaning device with optimized parameters causes less damage to root system and provides a more stable performance.Abstract. To solve the problems of poor working conditions, incomplete root systems, and low seedling-lifting efficiencies of apple orchard seedling-lifting machines, a new type of shaking soil-cleaning device was proposed, in which a spatial four-bar linkage (RSSR) was used instead of a traditional planar linkage. By means of the direction cosine matrix, the position and pose of the spatial four-bar mechanism of the device were analyzed, and the functional relationship was obtained. A fast Fourier transform (FFT) was used to synthesize a periodic function of the spatial four-bar linkage, a numerical atlas was established, and the dimensions were selected by means of fuzzy recognition. A genetic algorithm (GA) was used to optimize the identified parameters, and the optimized mechanisms was compared with the traditional planar linkage mechanism. The results showed that the maximum positive and negative errors of the first curve fitting groups were 0.43% and 0.67%, respectively, and those of the second curve fitting group were 0.79% and 0.50%, respectively, which met the operating and precision requirements. The structure of the new oscillating soil cleaning device is compact. Meanwhile, moderate lengths of the main roots, dense root hair, and complete root systems were achieved. The results showed that the taproots remained intact, and they were between 120 and 150 mm long. Due to the small sample size, the damage rate of the seedlings was zero, and the seedlings produced by the two models met the agronomic requirements. Thus, the requirements of agricultural operations are met by the optimized mechanism. This design concept can provide ideas for follow-up spatial RSSR four-bar mechanism design, and the optimized size parameters can provide a reference for the follow-up design and research of seedling and soil clearing devices. Keywords: Dimension synthesis, Genetic algorithm, Numerical atlas method, Oscillating soil cleaning device, Spatial RSSR mechanism.