The invention discloses a space-time hierarchical and operation-optimized method and system for the serial-parallel, cascade pumping station water delivery system. The method includes the steps that establish a complete set of space-time hierarchical and operation-optimized theoretical system for the serial-parallel, cascade pumping station water delivery system. It establishes successively in the space dimension, single level pumping station, serial system, parallel system operation-optimized model system; in the three-model system, it establishes successively the three layers of operation-optimized model: system operation efficiency, daily, mid-term and long-term, according to different optimization targets in the time dimension and considering the delays by the startups and shutdowns of the pumping station as well as other factors. It figures up a multi-layered optimized operation plan, and realizes the step-by-step optimized decomposition of the operation plan in the time (mid, long-term, daily, hourly) dimension and space (parallel system, serial system, single-level pumping station) dimension, including the distribution of water within different time periods, the optimization plan for the staircase hydropower, the optimized operation plan for the internal units of the pumping station. This method solves the tough problem of figuring up an optimized operation for the serial-parallel cascade pumping station water delivery system, due to the complications and dynamics of control and operations.