The invention discloses a city and town river and lake water ecological restoration method based on a new restoration mode of mud first and water second. The method is used for city and town river and lake bottom mud in-situ restoration and micro-ecological reconstruction, and comprises the following steps: synchronous reduction of anaerobic bottom mud carbon, nitrogen and sulfur pollutants is realized through SedCaN particles, based on microbial acclimatization and spreading, in-situ regulation of a bottom mud microbial community structure is realized, and construction of an aerobic microbial ecosystem is realized. According to the invention, the river and lake pollution in-situ treatment mode and method have the advantages of low energy consumption, low cost, higher efficiency, higher comprehensiveness and higher safety, can realize an in-situ treatment target of construction of a water body-bottom mud healthy ecological system and collaborative reduction of pollutants, can remove 95% of oxygen consumption pollution such as bottom mud sulfide and the like within 15 days, basically eliminates black and odorous bottom mud, solves the technical bottleneck that the natural environment of the polluted bottom mud is difficult to quickly recover by an aerobic process, shortens the construction period by more than 30 days, and can save the cost by more than 40-50%compared with a desilting scheme.