Territorial spatial governance is transferred to holistic governance and territorial spatial planning is transferred to holistic management planning under the modernization of the national governance system and governance capacity. To ensure the integration of research results of special planning and territorial spatial planning, promote the development of territorial spatial planning system, and raise the level of modernization of territorial spatial governance, a standardized research pattern for special planning should be formulated. This paper reconstructs the “standardized” water ecosystem resilience research pattern under the requirements of the territorial spatial planning system construction. Firstly, the research deficiencies of water ecosystem resilience evaluation, planning strategies, and planning implementation guarantee, will be summarized by reviewing the existing research. Secondly, the requirements of the territorial spatial planning system construction would be summarized and analyzed, which includes whole-process transmission, all-factors in whole-domain, whole-space coverage, and whole-cycle management. Then, a “standardized” water ecosystem resilience research pattern would be reconstructed, which includes the research procedure of water ecosystem resilience based on whole-process transmission, the evaluation system of water ecosystem resilience based on all-factors in whole-domain, the evaluation system of water ecosystem resilience based on whole-space coverage, and the planning implementation guarantee of water ecosystem resilience based on whole-cycle management. Finally, the technical path of a “standardized” water ecosystem resilience research pattern is proposed. The reconstructed research pattern provides the theoretical and methodological basis for empirical research and other ecosystem resilience research.