In order to study the impact of small space debris on the sandwich honeycomb structure panel of micro/Nano satellite with multi-layer insulation, taking the AIST satellite shell of Samara University as a reference, the deceleration effect of the sandwich honeycomb panel on the fragments when the debris hits the honeycomb core at different positions was studied by numerical simulation method, and the comparison with previous experiments was made. The simulation results showed that, compared to hitting the edge of the honeycomb or hitting the intersection of honeycomb core, when a 4 km/s projectile with a diameter of 2 mm hit the hollow of the honeycomb, the damage area to the honeycomb panel was much smaller than that of the former. The absorbed kinetic energy of the honeycomb panel was less, and the residual kinetic energy of the debris cloud was higher, leading a greater debris damage to the sensors inside the satellite. At the same time, the thickness and side length of the honeycomb core were adjusted while the areal density and the thickness of the panel partition remain unchanged, and the debris kinetic energy and the average debris velocity after deceleration were obtained by numerical simulation. Combining the probability of debris hitting each position of the honeycomb core and the corresponding residual kinetic energy, through mathematical expectation, the original design scheme is a relatively high-quality design scheme under the condition that the areal density and the thickness of each layer are unchanged.