Repetitive transcranial magnetic stimulation (rTMS) holds the ability to modulate the connectivity within the stimulated network. However, whether and how the rTMS targeted over the primary motor cortex (M1) could affect the connectivity within the sensorimotor network (SMN) is not fully elucidated. Hence, in this study, we investigated the after‐effects of rTMS over left M1 at different frequencies on connectivity within SMN. Forty‐five healthy participants were recruited and randomly divided into three groups according to rTMS frequencies (high‐frequency [HF], 3 Hz; low‐frequency [LF], 1 Hz; and SHAM). Participants received 1‐Hz, 3‐Hz or sham stimulation and underwent two functional magnetic resonance imaging (fMRI) scanning sessions before and after rTMS intervention. Using resting‐state functional connectivity (FC) approach, we found that high‐ and low‐frequency rTMS had opposing effects on FC within the SMN, especially for connectivity with subcortical regions (i.e., putamen, thalamus and cerebellum). Specifically, the reductions in connectivity between cortical and subcortical regions within cortico‐basal ganglia thalamo‐cortical circuits and the cognitive loop of cerebellum, and increased connectivity between cortical and subdivisions within the sensorimotor loop of cerebellum were observed after high‐frequency rTMS intervention, whereas the thalamus and cognitive cerebellum subdivisions exhibited increased connectivity, and sensorimotor cerebellum subdivisions showed decreased connectivity with stimulated target after low‐frequency stimulation. Collectively, these findings demonstrated the alterations of connectivity within SMN after rTMS intervention at different frequencies and may help to understand the mechanisms of rTMS treatment for movement disorders associated with deficits in subcortical regions such as Parkinson's disease, Huntington's disease and Tourette's syndrome.