Background: The permeability of blood-spinal cord barrier (BSCB) is mainly determined by the junction complex of adjacent endothelial cells, including tight junction (TJ) and adhesion junction (AJ), which can be severely damaged after spinal cord injury (SCI). Exercise training is a recognized method for the treatment of SCI. The destruction of the BSCB mediated by matrix metalloproteinase (MMP) leads to inflammation, neurotoxin production, and apoptosis of neurons. The failure of effective regeneration of new blood vessels is also an important reason for the difficulty of recovery after SCI. We introduced water treadmill training (TT) for the first time, which can help SCI rats successfully exercise, and we explored the role of TT in promoting the ability to exercise after SCI and its possible mechanism.Methods: Sprague-Dawley (200–250g) rats were randomly divided into three groups. SCI models were established and rats underwent TT after SCI. Animals were sacrificed 7 d or 14 d post-surgery. The degree of neurological deficit, water content, BSCB permeability, apoptosis, protein expression and ultrastructure of vascular endothelial cells (EC) were assessed by the Basso-Beattie-Bresnahan (BBB) motor rating scale, haematoxylin-eosin (HE) staining, Evans blue (EB) staining, TUNEL staining, Western blot (WB) experiments, and immunofluorescence and transmission electron microscopy (TEM). Results: Our experiments show that TT reduces the permeability of BSCB and decreased tissue structure damage. TT improved functional recovery and it has significant significance when compared with the M group after SCI; TJ and AJ proteins increased significantly after TT training in SCI rats. TT training reduced apoptosis induced by SCI. TT can promote angiogenesis and the expressions of MMP-2 and MMP-9 were significantly inhabited by TT after SCI.Conclusions: In this study, the results indicate that TT promotes functional recovery partly for the following reasons: (1) TT protects residual BSCB structure from further damage; (2) it promotes vascular regeneration; and (3) it inhibits the expression of MMP-2/9 to mitigate BSCB damage.