PMLSM(Permanent Magnet linear Synchronous Motor) has widely applied to industrial automations, machine tools and semiconductor equipments due to the merit on the reduction of noise, vibration and the superior dynamic characteristics in comparison to the conventional method, which uses mechanical transfer equipments. Especially, in the case of applying to Z-axis operation structure, control system needs the method of an initial angle setting and the improvement of up/down operation characteristics. This paper proposes an initial angle setting algorithm and a variable gain schedule using real speed and moving direction to improve up/down operation characteristics. The effectiveness of proposed algorithms Is demonstrated by comparing to a conventional gain system via 4-point absolute positions profile with each velocity, acceleration and deceleration.