Parallel processing, fast convergent motor model and characteristic points extracted from the smallest outer circle were proposed to design the automatic alignment system, which can integrated diagnostic fast automatic alignment. First, all the alignment steps were executed in parallel and serial-parallel mode, and the important steps were reduced to unit alignment model. Second, the mathematical model for fast automatic alignment was used and the fast convergent algorithm of the unit alignment model was implemented. Finally, according to the characteristics of small laser spot, which contrast was low, distribution was asymmetrical, spot was not complete, the 100 characteristic points were extracted from the smallest outer circle and any two points distance was maximal, then a new method of circle fitting using least square method to calculate small laser spot center was proposed. Through the improvement of the above three aspects, alignment time reduced from 40 minutes to 8 minutes before the three aspects were optimized, the error of small laser spot centre is less than 2 pixels, and meet the experiment requirements.