Objective To compare the diagnostic value of enhanced triple-phase computer tomography (CT) with enhanced magnetic resonance imaging (MRI) in small hepatocellular carcinoma (SHCC), and postoperative recurrent small lesions. Methods A total of 166 patients with suspected SHCC from Yongmei Group General Hospital between July 2021 and June 2024 were selected and divided into two groups: 83 undergoing enhanced triple-phase CT scanning were assigned to enhanced CT group, and 83 undergoing enhanced MRI were assigned to enhanced MRI group. Postoperative pathological results were used as the gold standard to compare the consistency, diagnostic efficacy, and imaging findings between the two groups. For postoperative recurrent small lesions, pathological examination was also used as the reference to compare the consistency and diagnostic efficacy of the two groups. Results In the enhanced CT group, 19 cases were positive and 64 cases were negative by detection, while postoperative pathology confirmed 26 cases of SHCC positive and 57 cases negative. In the enhanced MRI group, 37 cases were positive and 46 cases were negative by detection, while postoperative pathology confirmed 34 cases of SHCC positive and 49 cases negative. The sensitivity of the enhanced MRI group for diagnosing SHCC was 97.06%, with an accuracy of 93.98%,and the negative predictive value was 97.83%, which were higher than the sensitivity of 57.69%, accuracy of 81.93%, and negative predictive value of 82.81% in the enhanced CT group. The differences were statistically significant (χ2=14.270,5.685, 6.207, P<0.05). The consistency of diagnosis and pathological examination (Kappa value=0.877, P<0.001) in the enhanced MRI group was higher than that in the enhanced CT group (Kappa value=0.547, P<0.001). There were no statistically significant differences in specificity and positive predictive value between the two groups (P >0.05). The difference in arterial phase signals between the enhanced CT group and the enhanced MRI group was statistically significant (χ2=6.470, P<0.05), while no significant differences were observed in the portal vein phase and delayed phase signals (P>0.05). At the 5-month follow-up, diagnostic analysis was performed on 56 patients with detected suspected small lesions. In the enhanced CT group, 22 cases were positive for recurrent small lesions and 34 cases were negative, while postoperative pathology confirmed 27 cases of recurrent small lesions positive and 29 cases negative. In the enhanced MRI group, 32 cases were positive for recurrent small lesions and 24 cases were negative, while postoperative pathology confirmed 29 cases of recurrent small lesions positive and 27 cases negative. The sensitivity of the enhanced MRI group for diagnosing recurrent small lesions was 96.55%, with an accuracy of 91.07%, and the negative predictive value was 95.83%, which were higher than the sensitivity of 66.67%, accuracy of 76.79%, and negative predictive value of 73.53% in the enhanced CT group. The differences were statistically significant (χ2=8.513, 4.236, 4.905, P<0.05). The consistency of diagnosis of recurrent small lesions and pathological examination (Kappa value=0.821, P<0.001) in the enhanced MRI group was higher than that of the enhanced CT group (Kappa value=0.532, P<0.001). There were no statistically significant differences in specificity and positive predictive value between the two groups (P>0.05). Conclusion Enhanced MRI has higher diagnostic value than enhanced triple-phase CT for SHCC and superior sensitivity and accuracy in diagnosing recurrent small lesions.