The effect of Constraint-induced movement therapy (CIMT) or Intermittent theta-burst stimulation (iTBS) alone is limited in improving motor function after a stroke. In this study, we explored the efficacy and possible mechanisms in combination of CIMT and iTBS through behavioral evaluation, RNA sequencing, Golgi staining, transmission electronic microscope (TEM), high-performance liquid chromatography (HPLC), western blotting (WB) and immunofluorescence. Firstly, we observed that combination therapy is safe and effective, and it can significantly reduce the number of immature dendritic spines and increase the number of functional dendritic spines, the amount of glutamate (Glu) and the expression of Glu1 receptor (Glu1R). Meanwhile, we have found a significant reduction in neutrophil extracellular traps (NETs) in the combination group, and correlation analysis showed that the number of NETs is negatively correlated with the number of functional dendritic spines and the expression of Glu1R. After Cl-amidine ((S) - N - (1-amino-5- (2-chloroacetamiprid) -1-oxopentan-2-yl) benzamide 2,2,2-trifluoroacetate salt, PAD4 inhibitors) application, combined therapy did not further improve motor function and the expression of Glu1R. Our results proved that CIMT combined with iTBS therapy is a better therapeutic intervention. It improved motor function and synaptic plasticity after a stroke by promoting the transformation of functional dendritic spines and the expression of Glu1R in the ipsilateral primary motor cortex. The reduction of NETs generation is one of the key targets within it.