In the rapidly evolving e-commerce landscape, efficient packaging and logistics reduce costs and enhance customer satisfaction. This study addresses the problem of dynamic bin size optimization in e-commerce logistics by proposing a series of intelligent algorithms. Considering real-world constraints such as item separation requirements, a Mixed Integer Programming Model for Multi-Order Multi-Box Open-Dimension Rectangular Packing (MOMB-ODRPP) is formulated. The Stacked Clustering Algorithm (SCA) series, One-Dimensional Fixed Stacked Clustering Algorithm (ODF-SCA), Two-Dimensional Fixed Stacked Clustering Algorithm (TDF-SCA), and Variable Neighborhood Descent Spatial Ordering Algorithm (VND-SOA) series are employed to solve the MOMB-ODRPP model and improve order packing rates and optimize bin sizes. Computational experiments using real-world data from JD’s e-commerce operations reveal that the TDF-SCA algorithm series outperforms the ODF-SCA series by approximately 5% in Case 4. In contrast, the VND-SOA-S1 and VND-SOA-S2 algorithms achieve improvements of 0.83% and 0.76%, respectively, over the TDF-SCA-P2 algorithm in Cases 4 and 11. The comparative analysis highlights the practical implications of bin size optimization, with Case 11 providing a more viable option for standardizing bin sizes in e-commerce logistics.