The rapid development of electronic commerce has increased demands for order fulfillment efficiency, making this a crucial challenge for warehouse systems. The study proposes a novel fishbone robotic mobile fulfillment system (FRMFS) to optimize warehouse layout and enhance the picking efficiency of automated warehouse systems, such as robotic mobile fulfillment systems (RMFS). Through the construction and analysis of mathematical models, the research demonstrates that FRMFS can significantly reduce the travel distance of robots when compared to traditional RMFS. This leads to an improvement in the overall picking efficiency of the warehouse system. The study also examines the impact of warehouse parameters, cross-aisle angles, and the number of picking stations on system operational efficiency. Simulation experiments confirm that FRMFS can reduce picking distances by 18%–28% compared to traditional RMFS. This makes it particularly suitable for complex warehouse systems with high requirements for operational response time and system throughput. Furthermore, the study introduces a point-based layout design method for picking stations in FRMFS, demonstrating its efficiency as a heuristic approach. This research presents a scientific analysis framework and model support for the operational design and optimization of FRMFS, offering valuable insights for management practices.