Objectives The aim of this study was to evaluate the effect of microbubbles on the efficacy of transcranial doppler (TCD) ultrasound-assisted thrombolytic therapy of recombinant tissue-type plasminogen activator (rt-PA). Methods Male New Zealand white rabbits ( n = 36) were randomly divided into an rt-PA group ( n = 18) and an rt-PA plus microbubble group ( n = 18). After the cerebral infarction model was constructed with autologous blood clots, rt-PA and rt-PA plus microbubble intervention were performed, respectively. The hemodynamic changes and infarct size of the two groups were recorded. In addition, the ELISA method was used to detect the level of nitric oxide (NO), superoxide dismutase (SOD), and malondialdehyde (MDA) in the brain tissue of the two-group graph model and high-sensitivity C-reactive protein (hs-CRP) in the serum. Results In the rt-PA group, the recanalization rate was 38.9% and the average infarct size was 11.8%. In the rt-PA plus microbubble group, the recanalization rate was 66.7% and the average infarct size was 8.2%. In addition, the average values for NO, SOD, MDA, and hs-CRP were 16.48 ± 5.39 μmol/L, 730.2 ± 9.86 U/mg, 0.92 ± 0.43 nmol/mg, and 8.56 ± 1.64 mg/L in the rt-PA group, respectively, and the average values were 9.18 ± 3.37 μmol/L, 426.2 ± 6.39 U/mg, 0.73 ± 0.44 nmol/mg, and 5.23 ± 0.94 mg/L in the rt-PA plus microbubble group, respectively. Conclusions The addition of microbubbles enhanced the effects of TCD-assisted rrt-PA thrombolysis.