Embodiments of the invention provide a Burst mode based short pulse laser system and a control method thereof. The system includes an outer control circuit, an optical oscillation stage module, a pattern matcher and an optical amplifier module; the outer control circuit is used for generating a trigger signal and sending the trigger signal to the optical oscillation stage module so as to control the optical oscillation stage module; the trigger signal is a pulse electric signal and includes a pump trigger signal and a Q-switching trigger signal; the optical oscillation stage module is used forgenerating a narrow pulse laser according to the received trigger signal; the pattern matcher is used for adjusting the size of the narrow pulse laser and sending the size-adjusted narrow pulse laserto the optical amplifier module; and the optical amplifier module is used for performing amplification processing on the size-adjusted narrow pulse laser to generate a Burst mode based short pulse laser. Through the embodiments, the stable output of short pulse laser strings can be maintained under a wide range of work repetition frequencies, and pulse width can be approximately and stably unchanged.