Multiple digital watermarking is an important and challenging task in geographic information science and data security. Vector geographic data are a basic data format for digital geographic data storage, and the security protection of these data involves copyright protection and tracking. As part of the solution, existing digital watermarking algorithms have made contributions to vector geographic data protection. However, when vector geographic data flow through multiple units, they need to be marked to ensure that the original data are not destroyed during data processing. Existing single or multiple data watermarking algorithms often fail in the presence of data processing because the new watermarks overlay the old ones. Consequently, a multiple digital watermarking algorithm based on multiple QIM (quantization index modulation) is proposed. First, based on traditional quantization index modulation (QIM), a multiple QIM is proposed. Unlike traditional QIM, in multiple QIM, the process of quantization is executed multiple times depending on the number of watermarks. Then, the vertices are quantized into different quantization intervals according to the multiple QIM. Finally, multiple watermarks are embedded into different quantization intervals to reduce the interference among multiple watermarks, and the original watermarks are not needed in the process of watermark detection. We then conducted experiments to test the multiple watermark method’s robustness and capacity, with an emphasis on datasets with a lower data volume. The experimental results show that the proposed algorithm achieves good performance in terms of its robustness against common issues, such as vertices addition, data simplification, data cropping, and feature deletion; this holds true for both normal and small amounts of data. Additionally, it has a high multiple watermark capacity.