Previous studies have shown that sport experts are different from novices in functions and structures of the cerebellar sub-regions and the functional connectivity (FC) associated with the cerebellum, suggesting the role of the cerebellum on motor skill learning (MSL). However, the manipulation of individuals with different motor skills fails to exclude the effects of innate talents. In addition, individuals with higher motor skills often start with the MSL in their young ages. It is still unclear whether the effects regarding the cerebellum would be shown at one's adult age. The present study was to directly alter individuals' motor skills to investigate whether MSL (taking learning to play badminton as an example) in adulthood influences resting-state activity in the cerebellum. To this end, young adults without ball training experience were recruited as participants and were assigned randomly into the experimental group and the control group. Participants in the experimental group were asked to attend a badminton training course for 12 weeks, while the control group did not regularly attend any ball sports during this period. Resting-state functional magnetic resonance imaging (fMRI) was recorded before and after the training. Results showed that compared to the control group, the experimental group had smaller amplitude of low-frequency fluctuation (ALFF) in right cerebellar hemispheric VI and left VIII after training. For the experimental group, right hemispheric VIII had a stronger FC with left hemispheric IV-V, cerebellar vermal IX, left middle cingulate gyrus and right hippocampus after training. Taken together, these findings suggested that MSL, at least learning to play badminton in adulthood, reduces resting-state activity in different sub-regions in the cerebellum but increases FC between sub-regions of the cerebellum as well as between sub-regions of the cerebellum and cerebral cortices (e.g., middle cingulate cortex and hippocampus).