Thrombolytic therapy in the treatment of cardiogenic acute cerebral embolism caused by coagulated blood carries the risk of hemorrhagic complications, and there is a need to develop safer and more reliable treatment methods. Laser thrombolysis therapy, which utilizes the difference in energy absorption between the thrombus and the arterial wall, has shown promise as a new treatment method because it can selectively act only on the thrombus. It has not been applied clinically, however, and one of the main reasons for this is that its underlying mechanism has not been elucidated. We developed a pulse laser thrombolysis system for treating cerebral blood vessels that consists of a diode-pumped solid-state neodymium-yttrium aluminum garnet laser, which has excellent stability and maintainability and is suitable for clinical applications coupled to a small-diameter optical fiber. Moreover, we analyzed the mechanisms that occur during pulsed laser irradiation of transparent glass tubes and gelatin phantoms. We found that bubbles form as a thermal effect in addition to ablation of the pulsed laser irradiation. Furthermore, we detected no shock waves or water jets associated with the bubbles. We analyzed the bubbles' dynamics and growth rate, and their effect on a rabbit blood clot phantom. We concluded that the bubbles generated by the laser irradiation physically cut the thrombus and thereby had a thrombectomy effect. We believe that this study will clarify the mechanism of laser thrombolysis therapy and contribute greatly to the realization of its clinical application.