In-situ flying height (FH) testing of the magnetic head in hard disk drives (HDD) plays an essential role in the commercial availability of high-density magnetic storage technology. A symmetrical common-path heterodyne interferometry is proposed, which utilizes a traverse Zeeman laser and a high-speed phase measurement technology. It takes the advantages of direct in-situ traceable measurement with high resolution (0.1 nm) and high sampling frequency (100 kHz). The errors introduced by rotation of disk and environmental disturbance can be adaptively compensated. The system is also suitable for the simulative FH measurement using glass disk. The experimental results show that it is able to clearly describe the FH modulation of less than 10 nm when the dynamic pitch of the rotating rigid disk is 1.2 μm.