The present disclosure provides a method for aligning a master oscillator power amplifier (MOPA) system. The method includes ramping up a pumping power input into a laser amplifier chain of the MOPA system until the pumping power input reaches an operational pumping power input level; adjusting a seed laser power output of a seed laser of the MOPA system until the seed laser power output is at a first level below an operational seed laser power output level; and performing a first optical alignment process to the MOPA system while the pumping power input is at the operational pumping power input level, the seed laser power output is at the first level, and the MOPA system reaches a steady operational thermal state.