RSK2 (p90 ribosomal S6 kinase 2) is a serine/threonine kinase expressed in a variety of cancers. Molecular-targeted inhibition of RSK2 as a potential therapeutic strategy for human cancers has been documented. In this work, a series of isoindole-1,3-dione derivatives as novel RSK2 inhibitors were designed and synthesized from a hit discovered in our previously study. Some compounds were confirmed to be moderate potent RSK2 inhibitors with the IC50 values at about 0.5 μM range. Some compounds exhibited much improved inhibitory activity against RSK2 compared with the hit, the most active compound 7 inhibited RSK2 activity with an IC50 value up to 0.47 μM (inhibitory ratio of 97% at 10 μM). The structure-activity relationship (SAR) analyses and binding mode studies by molecular docking were performed for searching more potent RSK2 inhibitors.