As a crucial part of a high-speed polar coordinate laser writing system, the alignment of the rotatory stage axis and the writing laser optical axis has been a key point that influences the accuracy of the whole system and the fabrication patterns. An alignment method of the rotatory stage axis and the writing laser optical axis is proposed. An alignment system is established and the imaging subsystem is calibrated by a high precision calibration object. A circle center lookup algorithm is applied to find the axis of the rotary stage. The accuracy of the alignment could reach 400 nm. The results of the alignment indicate that the proposed alignment method is a good method for the alignment of the rotary stage axis and the writing laser optical axis. The proposed alignment is useful in the fields of high-resolution maskless laser lithography in polar coordinates.