Crossed cerebellar diaschisis (CCD) has been widely investigated in patients with supratentorial stroke. However, the role of CCD in lower limb recovery after stroke is still unknown. In this study, using a region-of-interest-based analysis of diffusion tensor imaging (DTI), a total of 44 cases of stroke within 3 months onset were enrolled for assessment of the cerebral peduncle (CP) and middle cerebellar peduncles (MCP) in CCD. Compared with the control group, the fractional anisotropy ratio (rFA) and laterality index (LI) of the CP and MCP in the stroke group significantly decreased. The rFA of the MCP (unaffected side/affected side) showed a more significant correlation with 1-year paresis grading (PG), lower extremity PG, upper extremity PG, National Institutes of Health Stroke Scale (NIHSS), and functional independence measure (FIM) motor item score, in comparison to the rFA of the CP (affected side/unaffected side) (r = −0.698 vs. r = −0.541, r = −0.651 vs. r = −0.386, r = −0.642 vs. r = −0.565, r = −0.519 vs. r = −0.403, and r = 0.487 vs. r = 0.435, respectively). Furthermore, the LI of the CP had a more significant association with 1-year Brunel Balance Assessment (BBA), upper extremity PG, and Modified Rankin Scale (mRS) as compared to the LI of the MCP (r = 0.573 vs. r = 0.452; r = −0.554 vs. r = −0.528; and r = −0.494 vs. r = −0.344, respectively). We set the cutoff point for the MCP rFA at 0.925 (sensitivity: 79% and specificity: 100%) for predicting lower extremity motor function prognosis and found the receiver operating characteristic (ROC) curve of MCP rFA was larger than that of CP rFA (0.893 vs. 0.737). These results reveal that the MCP may play a significant role in the recovery of walking ability after stroke.