An alignment-free sensing module for the positioning system based on tunneling magnetoresistive (TMR) sensors with an absolute-incremental-integrated scale is demonstrated. The sensors of the proposed system for both lines consist of identical layer stacks; therefore, all sensors can be fabricated in identical processes from thin film deposition to device patterning on a single substrate. Consequently, the relative position of the sensors can be predefined at the lithography stage and the alignment error between sensors caused by the manual installation is completely eliminated. Different from the existing sensing scheme for incremental lines, we proposed to utilize the magnetic tunnel junctions with a perpendicular anisotropy reference layer and an in-plane anisotropy sensing layer. The sensors are placed parallel to the scale plane with magnetization of the sensing layer in the plane, which show the capability of polarity detection for the absolute line and reveal sinusoidal output signal for the incremental line. Furthermore, due to the large signal of TMR, the working distance can be further improved compared with conventional sensors. In addition, the cost of the positioning system is expected to be lowered, since all the sensors are fabricated in the same process without extra installation. Our design may pave a new avenue for the positioning system based on a magnetic detection scheme.