The sustained effects of acupuncture have been widely applied to clinical treatment, thus it can be assumed that the relatively functional specificity of acupoints may evolve as the function of time. In this study, we originally combined ICA and multivariate Granger causality analysis to explore the causal interactions within and among the post-acupuncture resting-state networks (RSNs) at a hearing-related acupoint GB40, with the cognition-related acupoint KI3 as a control. Following acupuncture at GB40, the superior temporal gyrus (STG) and anterior insula (AI) within auditory network appeared persistent bidirectional connection with maximal strength, and the interactions between the auditory network and others became more complex as time passed. For KI3, both the superior parietal lobule (SPL) and dorsolateral prefrontal cortex (DLPFC), as vital nuclei of cognitive function, emerged increased causal outflows and inflows as time went on. We concluded that acupuncture at different acupoints may exert different evolutive effects on causal interactions within and across the RSNs during segmented post-stimulus resting states.