The invention relates to a method for calculating propagation characteristics of high altitude electromagnetic pulse (HEMP) in seat water. The method comprises the steps of, firstly, obtaining initialization parameters; secondly, calculating the dielectric constant of the sea water; thirdly, calculating the sea level reflective transitive function; fourthly, calculating the sea water transmission loss transitive function; fifthly, calculating the sea water total electromagnetic pulse transitive function. The method for calculating the propagation characteristics of the high altitude electromagnetic pulse in seat water can help calculate the electromagnetic pulse environment at any sea water depth as the input conditions of anti-electromagnetic pulse design of an undersea electrical system and meanwhile can help guide start and stopping of the undersea electrical system in real time.