Logistics is playing a significant role in supporting economic growth and material security during the epidemic period and it has been experiencing a rapid development in recent years. With the issues of personalisation and cost, the economy and society ask for higher requirements for logistics storage systems. The rational design of the functional area layout is an essential step to improve the operational efficiency of the logistics warehousing system. In reality, due to warehouse design and equipment application, there has been a gradual increase in irregular warehouses. By taking an irregular warehouse as an example, combining the operation status quo, this paper clarifies the functional area settings and constructs a 0–1 integer planning model based on the grid and systematic layout planning method with constraints, such as the unique functional attributes of the grid. We optimised the genetic algorithm based on the warehouse irregularity factor and the grids factor, and then solve it through MATLAB. Finally, by using the Flexsim software, simulation metrics were selected for evaluation, the method feasibility is verified.