An iris diaphragm actuator includes a magnetic position sensing structure, at least one driving element and a light intercepting element. The magnetic position sensing structure includes a magnetic element and a magnetic sensor relatively disposed. The driving element connects and drives the magnetic element or the magnetic sensor to perform a rotating motion with respect to a rotation center such that the distance and angle between the magnetic element and the magnetic sensor are changed so as to obtain a substantially linear relation between a magnetic flux sensed by the magnetic sensor and the position of the magnetic element. Also, an arrangement method of a magnetic position sensing structure is disclosed.