A method and system for generating a logarithmic non-uniform pseudo-random electromagnetic exploration signal including: constructing two or more basic unit signals, according to an exploration requirement, that are stairstep signals obtained by superposing in-phase periodic square wave signals, a frequency ratio between adjacent periodic square wave signals is 2, and the two or more basic unit signals meet the following requirement: if a lowest dominant frequency in a first basic unit signal is a fundamental frequency, lowest frequencies of the remaining basic unit signal are l×2m times the fundamental frequency, where l is an odd number except 1, and m is a natural number; and superposing the two or more basic unit signals to obtain a logarithmic non-uniform 2n sequence pseudo-random signal. A logarithmic non-uniform 2n sequence stairstep signal is constructed within a limited frequency interval, and requirements of prospectors for a higher frequency density within a specific frequency interval are met.