Helical core optical fiber is used to achieve high power fiber laser output and polarization state control, and it has become a hot issue of current research due to its unique characteristics of chiral medium. The key difficult point is critical concentric alignment between the actual rotational center and the optical fiber core in helical core fiber manufacturing process. This paper proposed a new alignment method based on the coordinates of centroid. That is, injecting light to the main and sub fiber core which is fixed on the rotating clamping apparatus, acquiring two coordinates of the energy center in output field spot image with the help of the microscopic imaging system by using the squared weighted centroid method. X-axis is defined as the two fiber core connection direction, which perpendicular direction is Y-axis, and the origin is the center of main fiber core, so the correspondence between the main fiber core XY coordinate system and the rotating clamping apparatus X0Y0 coordinate system is available. Main fiber core rotation center coordinates X'Y' can be obtained by fitting, and the X0Y0 adjustment of clamping apparatus can be also acquired by coordinate transformation. Experimentally measured eccentricity error can be controlled around 8μm, which achieved concentricity precise adjustment. The experimental device has advantages of small size, stable performance, high positioning accuracy, and this method overcomes the key technical difficulties of the helical core optical fiber preparation.