To study the clinical effects of scalp acupuncture plus low frequency rTMS in hemiplegic stroke patients. A total of 28 hemiplegic stroke patients were recruited and randomly assigned to the experimental group (scalp acupuncture low frequency rTMS routine rehabilitation treatment) or the control group (scalp acupuncture routine rehabilitation treatment). All patients received a diffusion tensor imaging examination on the day of admission and on the fourteenth day. Compared with pre-treatment, the upper limb motor function score and ability of daily life score increased significantly in the two groups, and motor function improvement was much greater in the experimental group. Fractional anisotropy values significantly increased in white matter tracts, such as the corticospinal tract, forceps minor, superior longitudinal fasciculus and uncinate fasciculus in the two groups. Compared with pre-treatment, the fractional anisotropy values increased and mean diffusion values decreased synchronously in the forceps minor, left inferior fronto-occipital fasciculus, left inferior longitudinal fasciculus, left superior longitudinal fasciculus and left uncinate fasciculus in the experimental group. Before and after treatment, there were no significant differences in the changes of fractional anisotropy values between the two groups, but the changes of the mean diffusion values in the experimental group were much greater than those in the control group in the left superior longitudinal fasciculus and the left uncinate fasciculus ($p<$ 0.05). Moreover, the increased fractional anisotropy values in the forceps minor in the experimental group were significantly positively correlated with the increased Fugl-Meyer assessment score. Our study concluded that based on routine rehabilitation treatment, scalp acupuncture plus low frequency rTMS can promote white matter tracts repair better than scalp acupuncture alone; the motor function improvement of the hemiplegic upper limb may be closely related to the rehabilitation of the forceps minor; the combination of scalp acupuncture and low frequency rTMS is expected to provide a more optimal rehabilitation protocol for stroke hemiplegic patients.