It is important to determine and distinguish the mechanisms underlying different types of pain because different drug targets are useful in pain of different origins. Specific low back pain (SLBP) with a recognizable pathology and nonspecific low back pain (NSLBP) are different pain conditions. The amygdala has been linked with the pathophysiology of chronic LBP. However, it is not known whether the amygdala is differentially affected in both conditions. Our study suggested that the amygdala morphology, resting-state functional connectivity and effective connectivity are differentially affected in subjects with SLBP and NSLBP, indicating different brain mechanisms in SLBP and NSLBP.