Water rights management modeling was considered the useful measure to ensure efficient water resources allocation and to avoid intensifying conflicts over water rights. Regarding to the two major patterns of water rights across the world, namely, quantitative water rights (QWR) and duration-based water rights (DWR), the corresponding measures are fastidious. Since QWR was established to set water entitlements instead of DWR in Heihe River Basin, China, the disability of usual DWR tool, managing water diversion by water intakes closing (WIC) during a certain period, has arisen increasingly. The historical data also reflected the low reliability of DWR in allocating water resources quantitatively without modeling guidelines. Aimed at the challenge, a modeling framework and a mixed integer optimization model (MIOM) combing QWR objectives and DWR tools were developed, by which the optimal schemes in Pareto frontier were found to improve the water intake on/off events, including WIC stages, duration days, and starting date through long term series probability analysis and historical data. Results showed that the reliability of DWR allocation was enhanced and WIC duration was reduced significantly compared with current regulation. Scenario analyses indicated that MIOM was powerful for assisting DWR tool to manage QWR and the proposed framework was able to manage water rights efficiently in comparable basins.