The invention discloses a shale formation isochronous comparison method and system. The method includes the following steps that: K-bentonite is accurately identified on the basis of a drilling core or a field outcrop; a contrast mark is determined on the basis of the K-bentonite; and formation stratification and dating experimental testing are performed based on the contrast mark, so that the geological age of the K-bentonite at the top and bottom of each stratum is determined; and inter-well or outcrop formation isochronous comparison is carried out on the basis of the contrast mark and theformation stratification, so that the isochronal grid of a shale formation area is established. According to the shale formation isochronous comparison method and system of the invention, the characteristics of the K-bentonite are utilized, and the fineness and precision of shale formation isochronous contrast can be improved.