Cross-sectional area (CSA) and signal intensity ratio (SIR) of the multifidus muscle (MFM) on magnetic resonance imaging (MRI) was used to evaluate the extent of injury and atrophy of the MFM in patients with negative treatment outcomes following microlumbar discectomy (MLD). Negative treatment outcome was determined by pain score improvement of <50% compared to baseline. Patients in groups 1, 2, and 3 were evaluated at <4 weeks, 4–24 weeks, and >24 weeks postoperatively, respectively. The associations between the follow-up, surgery time and the changes in the MFM were evaluated. A total of 79 patients were included, with 22, 27, and 30 subjects in groups 1, 2, and 3, respectively. The MFM SIR of the ipsilateral side had significantly decreased in groups 2 (p = 0.001) and 3 (p < 0.001). The ipsilateral MFM CSA significantly decreased postoperatively in groups 2 (p = 0.04) and 3 (p = 0.006). The postoperative MRI scans found significant MFM changes on the ipsilateral side in patients with negative treatment outcomes regarding pain intensity following MLD. As the interval to the postoperative MRI scan increased, the changes in CSA of the MFM and change in T2 SIR of the MFM showed a tendency to increase.