Fiber lasers have been widely used in surgery with the development of fiber photonics. Since the human body is prone to myocardial infarction caused by blood clots, laser thrombolysis was proposed as a safe and efficient treatment. Mode-locked fiber lasers have high peak power and narrow pulse width. In order to observe the effect of laser thrombolysis with mode-locked fiber lasers, a 1.5 µm mode-locked fiber laser based on carbon nanotubes was built, showing a pulse width of 1.46 ps, a 3 dB bandwidth of 1.65 nm, and a repetition rate of 29.5 MHz. The output pulses were amplified by an erbium-doped fiber amplifier to the hundred-milliwatt level and were applied to the surface of a self-made thrombus. The influences of lasing power and time on the damage diameter of the thrombus surface were evaluated. A low threshold damage power of 45 mW was observed, which resulted from the high peak power of the mode-locked pulses. These results demonstrate that high ablation efficiency can be achieved by using mode-locked pulses with a narrow pulse width and high peak power.