Based on the ecological problems in the inland river basin of the arid regions, the paper puts forward the significance of conducting integrated approach on ecological and hydrological processes to meet the development direction of earth system science and the state demand. Integrated study of ecological and hydrological processes is baseline of water resources management. It can lay foundation for balancing water for human being and nature. Taking the Heihe river basin for an example, the paper has reviewed the previous study in the basin. Data and knowledge have been accumulated in large quantities from investigation to monitoring, from data assimilation to modeling. They have provided with precondition to carry out Integrated study in the basin. Despite all these, we still face many challenges such as scale transform, applicability of models and coupling human activities into ecological and hydrological processes. For further study, three main study areas in future will be focused on: (1) to reinforce integrative monitoring of ecological and hydrological processes; (2) to improve the knowledge of human dimensions of regional environmental change; (3) to develop models or apply ecological and hydrological models in the basin.