Objective To investigate the predictive value of combined detection of serum complement C1q tumor necrosis factor-related protein 3 (CTRP-3), matrix metalloproteinase-9 (MMP-9), and tumor necrosis factor receptor-associated factor 6 (TRAF6) levels for hemorrhagic transformation (HT) after thrombolysis in patients with acute cerebral infarction. Methods A total of 107 patients with acute cerebral infarction admitted to the First People's Hospital of Nanyang City from January 2021 to January 2024 were selected. They were divided into the HT group (22 cases) and the non-HT group (85 cases) based on whether HT occurred within 24 hours after thrombolysis. The levels of serum CTRP-3, MMP-9, and TRAF6, as well as the National Institutes of Health Stroke Scale (NIHSS) scores, were compared between the two groups at admission, and their correlation was analyzed. The predictive value of combined serum indicators detection for HT occurrence after thrombolysis and the incidence of HT in patients with different serum levels after thrombolysis were also analyzed. Results Compared with the non-HT group, the HT group had lower serum CTRP-3 levels, higher serum MMP-9, TRAF6 levels, and NIHSS scores, with statistically significant differences (P<0.05). Serum CTRP-3 levels were negatively correlated with NIHSS scores, while serum MMP-9 and TRAF6 levels were positively correlated with NIHSS scores, with statistically significant differences (P<0.05). The area under the curve (AUC) for the combined prediction of post-thrombolysis HT using serum CTRP-3, MMP-9, and TRAF6 levels was 0.934, with a Youden's index of 0.744, and sensitivity and specificity of 90.91% and 83.53%, respectively, with statistically significant differences (P<0.05). The risk of post-thrombolysis HT in patients with high levels of serum CTRP-3, MMP-9, and TRAF6 was 0.113 times, 12.487 times, and 8.172 times than that in patients with low levels, respectively, with statistically significant differences (P<0.05). Conclusion The levels of serum CTRP-3, MMP-9, and TRAF6 are associated with the occurrence of HT after thrombolysis in patients with acute cerebral infarction. Combined detection of these three factors can provide a reference for clinical prediction of HT after thrombolysis in patients with acute cerebral infarction.