Mapping the brain alterations post stroke and post intervention is important for rehabilitation therapy development. Previous work has shown changes in functional connectivity based on resting-state fMRI, structural connectivity derived from diffusion MRI and perfusion as a result of brain-computer interface-assisted motor imagery (MI-BCI) and transcranial direct current stimulation (tDCS) in upper-limb stroke rehabilitation. Besides functional connectivity, regional amplitude of local low-frequency fluctuations (ALFF) may provide complementary information on the underlying neural mechanism in disease. Yet, findings on spontaneous brain activity during resting-state in stroke patients after intervention are limited and inconsistent. Here, we sought to investigate the different brain alteration patterns induced by tDCS compared to MI-BCI for upper-limb rehabilitation in chronic stroke patients using resting-state fMRI-based ALFF method. Our results suggested that stroke patients have lower ALFF in the ipsilesional somatomotor network compared to controls at baseline. Increased ALFF at contralesional somatomotor network and alterations in higher-level cognitive networks such as the default mode network (DMN) and salience networks accompany motor recovery after intervention; though the MI-BCI alone group and MI-BCI combined with tDCS group exhibit differential patterns.