A method and system for generating a high-order pseudo-random electromagnetic exploration signal. The method includes: constructing two or more basic unit signals according to an exploration requirement, wherein the basic unit signals are stairstep signals obtained by superposing a plurality of in-phase periodic square wave signals, and a frequency ratio between adjacent ones of the plurality of periodic square wave signals is 2; and superposing the two or more basic unit signals to obtain superposed stairstep signals, and correcting amplitudes to be consistent with amplitudes of the periodic square wave signals, to obtain high-order 2n sequence pseudo-random signals. The 2n sequence stairstep signals of different orders can be constructed within a limited frequency interval.