Aimed at the four problems in the process of water environmental management in watersheds in China, namely ambiguous logic of comprehensive management, unscientific differentiation for management units, mismatch between technical solutions and management units and insufficient connection among management units, the leading concepts of water environmental management in watersheds in the new era is proposed, namely “lasting management effect”, “economic management cost” and “global management system”; four steps of water management method in watersheds in the new era is put forward, including “systematic diagnosis”, “block decomposition”, “matching treatment” and “optimal effect”. The corresponding technology subsystems are classified into source control, process blocking and end governance according to the spatial dimensions, and pollution control and ecological remediation according to the temporal dimensions. The technology system of water environmental management in watershed in the special field is also proposed.