Non-point source (NPS) pollution has wide range of sources. Under rainfall conditions, NPS pollution occurs mainly by overland flow, resulting in difficult governance. In this study, based on the cooperative analysis of critical periods (CPs) and critical source areas (CSAs), a preferred hierarchical control strategy of NPS pollution, which was connected with management units, was proposed in the Danjiangkou Reservoir Basin (DRB) to improve the pertinence of NPS pollution control. The practicality of the grid-based CSA identification results was improved by point density analysis (PDA). CPs, sub-CPs, and non-CPs were identified on the temporal scale; CSAs, sub-CSAs and non-CSAs were identified on the spatial scale. The results showed that CPs (July, April, and September), sub-CPs (May, March, and August), and non-CPs contributed 62.8%, 31.1%, and 6.1% of the annual TP loads, respectively. Furthermore, we proposed a hierarchical NPS pollution control strategy: class Ⅰ (CSAs in CPs) → class II (sub-CSAs in CPs, CSAs in sub-CPs) → class III (non-CPs, non-CSAs, sub- and non-CSAs in sub-CPs). Class Ⅰ covered the periods and areas with the highest NPS pollution loads, contributing 26.2% of the annual load within 14.5% of the area and 25.0% of the time. This study provides a reference for the targeted control of NPS pollution at regional scale, especially in environmental protection with limited funds.