To implement dual-pickup-head multilayer data storage system, it is necessary to measure the synchronizing focus error of the two pickup heads to validate the feasibility of the focus servo method. By using the ABCD transforming matrix method of the geometric optics, we calculate the relationship between the output energy and the space interval of the two pickup heads. After confirming the detection system working in linear area, the coil motors of the two pickup heads were driven by sine signal with different frequency and record the output signals of the photo-detector under different movement states respectively, such as rest, single pickup head movement and dual-pickup-head synchronizing movement. The synchronizing focus error, which is caused by the characteristic parameter mismatch of the two pickup heads, could be obtained through frequency-domain analysis of these output signals. The experimental result shows that the amplitude of synchronizing focus error under 20 Hz is less than 1 μm, which could satisfy the focus servo requirement of the multilayer data storage system well.