The hydro-ecological response of rivers is crucial for determining ecological flow thresholds. To address the issues of lack of ecological data and challenges of ecological modeling in current research, the BHM-EcoFlow (Bayesian hierarchical modelling-ecological flow) model is introduced. Based on the prior knowledge and measured data from different river sections and different stations in the same river section, this model is able to simulate the hydro-ecological response of the entire river, due to the effective utilization of short-series data. Then, a case study of the mainstream of the lower-middle Hanjiang River in the year of 2011 is conducted to discuss the relationship between phytoplankton cell density, flow rate, and mixed layer temperature. In addition, the phytoplankton cell density in each river section under various flow conditions is further calculated. The results show that the BHM-EcoFlow model improves the applicability of short-series data and demonstrates a strong ability to identify complex hydro-ecological responses in the lower-middle Hanjiang River. This study can provide a technical support for the further calculation of environmental flow rate.