The embodiment of the invention discloses a method and a system for effectively correcting propagation delay of an ocean-crossing tsunami, creatively considers a second-order physical effect ignored by a shallow water equation, deduces a novel wave dispersion relationship based on a new physical framework, and improves the propagation delay of the ocean-crossing tsunami. Finally, the influence of wave dispersion, earth elasticity, seawater density stratification and other effects on the tsunami phase velocity is simulated through a depth correction method, so that the arrival time error of the oversea tsunami is reduced. Compared with a classic shallow water equation, the method has the advantages that delay errors of the ocean crossing tsunami are effectively corrected, and the tsunami propagation arrival time errors can be increased by 60-80%. Compared with other methods, the calculation efficiency can be improved by dozens of times or more on the premise that the calculation precision of the result obtained through the method is equivalent. Therefore, the method is particularly suitable for upgrading the tsunami early warning system.