Abstract: Focused Laser Differential Interferometer (FLDI) has been widely used in the spatial measurement of hypersonic boundary layer instability. However, at present, the FLDI system used in China can only measure the density change of one or two spatial points at a time, and the experimental measurement along the streamwise direction or normal direction in the boundary layer cannot be carried out efficiently, and the correlation of the density fluctuation signal between the two measuring points obtained from two wind tunnel runs is poor. In this work, a setup of multi-point FLDI measurement system is designed and built, which can simultaneously obtain the second mode instability waves characteristics of multiple measuring points in the hypersonic boundary layer in a single wind tunnel operation period. Based on the Φ0.25 m low noise Mach 6 hypersonic Ludwieg tube wind tunnel in Huazhong University of Science and Technology (HUST), the instability waves measurement experiment of a sharp cone’s boundary layer with a freestream Reynolds number of 1.19 × 10⁷ m⁻¹ is carried out by using the multi-point FLDI measurement system. The experimental results show that the multi-point FLDI system successfully captures the typical second mode instability waves with the main frequency in the range of 316.4−322.3 kHz, which is agree with the main frequency 319.3 kHz of those measured by a PCB sensor at almost the same measuring point. Furthermore, through the cross-correlation analysis of the density fluctuation data obtained based on the multi-point FLDI system, it is found that the phase velocity of the instability waves between the adjacent measuring points is the same, which is consistent with the propagation velocity characteristics of the second mode instability waves in the boundary layer. The experimental results verify the data obtained by multi-point FLDI are quiet reliable. Above all, the multi-point FLDI system has the advantages of high efficiency, low cost, high accuracy and high spatial resolution, so it is expected to be applied to the basic research investigation in the future, such as hypersonic boundary layer instability and receptivity mechanism.