In this paper, Embedded Large Eddy Simulation (ELES) is used to study the separated flow behind an axisymmetric afterbody of rocket. The impacts of grooves added to the end of main body for passive load control are discussed. Three cases include the original after-body without groove (Prototype), with 6 grooves in azimuthal direction (Groove6), and with 12 grooves (Groove12) are compared and analysed. The pressure fluctuation on the after-body wall are analysed by using the Proper Orthogonal Decomposition (POD) method. The results show that the added grooves at the trailing edge can promote the flow mixing in the shear layer, so that the size of the separated flow zone with high pressure fluctuation is reduced in the flow direction, which is beneficial to improve the stability of the afterbody. The POD analysis is focused on the anti-symmetric mode (m=1) which characterizes the azimuthal instability. The results show that the energy proportion of the single helical mode (m=1) decreases in Groove6 and Groove12 cases, and the decrease is relatively significant in Groove6 case. This mode is an antisymmetric mode, and reducing its energy proportion is beneficial to improve stability.