An image processing apparatus and an operation method of an endoscope system capable of emphasizing a change in color of a mucous membrane or the like which may occur at atrophy of the stomach due to atrophic gastritis are provided. Calculates a first signal ratio (-log (B / G)) between the B image signal and the G image signal and calculates a second signal ratio (-log (G / R)) between the G image signal and the R image signal . The difference between the first and second signal ratios within the first range and the first and second signal ratios within the second range is enlarged so that the difference between the normal mucosa and the abnormal area (atrophic mucosa area, deep vascular area) And emphasizes the color difference. The image after color difference emphasis is displayed on the monitor.萎縮性胃炎による胃の萎縮時に起こり得る粘膜等の色の変化を強調することができる画像処理装置及び内視鏡システムの作動方法を提供する。 B画像信号とG画像信号間の第1信号比(-log(B/G))を算出し、G画像信号とR画像信号間の第2信号比(-log(G/R))を算出する。第1範囲内の第1及び第2信号比と、第2範囲内の第1及び第2信号比との差を拡大して、正常粘膜と異常領域(萎縮粘膜領域、深層血管領域)との色差を強調する処理を行う。色差強調後の画像はモニタに表示される。