Neotectonic activity and history of the Yilan-Yitong fault, a main branch of the northern segment of the Tan-Lu fault zone remain controversial. Our detailed field investigation demonstrates that active faults are widely present in the Yilan-Yitong fault. They are composed of two main NE-striking active faults called the eastern and western active faults respectively and developed along boundary faults of the Paleogene graben. The active faults mainly show the crashed-type texture and reverse dextral slip. Stress inversion from many fault-slip data of the active faults show that Quaternary activity of the faults took place under the E-W compression that transformed into NEE-SWW compression at present. Our field observation and 14 C dating, in combination with previous dating results and earthquake distribution, suggest that the most recent periods of activity on the western active fault show alternation of Holocene and Late Pleistocene whereas those on the eastern active fault are dominated by Early-Middle Pleistocene. The active faults in the Yilan-Yitong fault present differential activities that show more intense activity on the western fault than on the eastern one, younger activity on the western fault, alternation of intense and weak activity, change in the most recent periods of activity along their strike as well as inhomogeneous distribution of earthquakes. Segmentation and differential activities of the faults along their strike mainly result from cutting of NW-striking faults on them.