The separation process of multi-spheres in hypersonic flow has been experimentally investigated. The experiments were conducted in a shock tunnel at a nominal freestream Mach number of 6. Iron or acetal small light spheres with different sizes, varying from 2.38 to 6 mm, were considered. They were mounted by a thin wire. The trajectory of the spheres was analyzed using optical images. By varying the radius and the number of spheres from a single to multiple spheres, the lateral velocity and the separation behavior including the phenomenon known as ‘shock wave surfing’ were measured and analyzed. A new equation to account for the lateral velocity of the multi-spheres was proposed by extending the well-known Passey and Melosh’s theory based on two bodies. The theoretical results were compared with the presented experimental data and a good agreement was found. Using the derived equation, the re-entry trajectory analysis of multi-spheres, that is regarded as the hypothetical break-up, was performed. The ground footprint and downrange due to the separation of the multi-spheres were compared with that of single- and two-spheres. The results showed that as the number of spheres increased, the lateral velocity increased while the ballistic coefficient decreased. This led to a large discrepancy in the ground footprint as well as the downrange when compared to the single sphere. Caution should therefore be exercised in the trajectory analysis when the effect of separation induced due to fragmentation is not considered.