The fully automatic pathological slide-stainer has significant implications for the digitization and simplification of pathology. Given that the current layout of slide-stainer is manually arranged, there are issues with inaccuracy and low time utilization. The purpose of this study is to design an algorithm for optimizing the layout of slide-stainer, aiming to achieve a scientifically arranged layout of staining sites. This enhances the efficiency of pathological section staining and ensures the timely completion of staining tasks. This paper first elaborates on the issue of staining sections using fully slide-stainer and proposes a mathematical model for the optimization design of the slide-stainer layout based on the problem. A multi-objective and multi-constraint optimization function is constructed. By simulating the daily process of section staining with the commonly used HE staining method in medicine, the optimal structure for layout optimization under these conditions is determined. The feasibility of this layout for regular use is verified through a variable neighborhood search algorithm. The results indicate that the optimized layout under this algorithm exhibits better work efficiency.