Complex regional pain syndrome (CRPS) type 1 is a chronic pain condition whose pathogenesis involves changes in the central and peripheral nervous systems, with potential genetic contributions. Functional magnetic resonance imaging (fMRI) studies report that alterations in resting-state functional connectivity (rsFC) may reflect central nervous system anomalies in CRPS type 1. Herein, we describe the case of a father and son with CRPS type 1 who exhibited different rsFC patterns in fMRI analyses correlating with their individual CRPS phenotypes. A 39-year-old male and his 61-year-old father presented with severe pain and mobility limitations in their right upper limbs following a vehicle accident and a fall, respectively, and were diagnosed with CRPS type 1. Despite receiving treatment, they experienced severe pain and limited mobility. The son exhibited dystonia and musculoskeletal atrophy while the father experienced extensive sensory disturbances. Bone scintigraphy revealed increased uptake in affected regions. The patients' resting-state fMRI data were compared with those of 48 healthy adults using the CONN software, with the false discovery rate set at p<0.05. Distinct brain regions for the father and son exhibited decreased rsFC (between the rostral prefrontal cortex and orbitofrontal cortex in the father and between the supplementary motor area and pallidum in the son; all in the right hemisphere). These changes corresponded to pain sensation and cognitive-emotional alterations in the father and limb movement disorders (dystonia) in the son. Our findings strongly support the idea that abnormalities in rsFC are closely linked to CRPS type 1 phenotypes.