The invention relates to a method of cleaning and maintaining a seawater taking pipeline by means of strong brine and fresh water. The method comprises a pipeline cleaning method and a pipeline maintaining method. The pipeline cleaning method successively comprises the three steps of strong brine positive pressure soaking cleaning, fresh water positive pressure soaking cleaning and seawater taking pipeline flushing. The pipeline maintaining method successively comprises the two steps of strong brine positive pressure soaking maintaining and seawater taking pipeline flushing. The step of strong brine positive pressure soaking cleaning comprises the following steps: firstly, inputting ozone in strong brine by jet-flow aeration; then injecting the strong brine into the seawater taking pipeline from the water outlet of the seawater taking pipeline; and keeping a positive pressure at the water taking port soaked in seawater. The invention also provides a corresponding system. A positive pressure environment is established in the seawater taking pipeline, and the salinity of a flushing medium is increased acutely and then reduced acutely, so that growth and development of various zooplankton and phytoplankton in the seawater taking pipeline can be effectively inhibited; excessive strong brine and fresh water are effectively prevented from being discharged into sea due to the low positive pressure environment of the water taking port, and damage on the marine environment is reduced to the minimum extent.