To implement a dual-pickup-head multi-layer 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 geometric optics, we calculate the relationship between the output energy and the space interval of the two heads. After confirming the detection system working in the linear area, the voice coil motors of the two pickup heads were driven by sine signals with different frequencies and recorded the output signals of the quadrant photodetector under different movement states respectively, including static, lower pickup head movement and dualpickup-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 mm, which could adequately satisfy the focus servo requirement of the multi-layer data storage system.