The phosphoinositide 3-kinase (PI3K) pathway playing an important role in cell proliferation, growth, and survival is one of the most frequently dysregulated pathways in cancer. However, PI3K inhibitors, used as a monotherapy, have shown limited therapeutic efficacies and high rates of side effects from acquired resistance to PI3K inhibition via feedback loop-mediated pathway reactivation and poor tolerability of small-molecule inhibitors. Here, we proposed a multi-targeting siRNA delivery system using polymerized siRNA-based nanoparticle formulations (Msi-NPs) as a PI3K-targeted anticancer therapy for simultaneous ablation of Rac1 and p110β-subunit of PI3K linked by a Rac-PI3K positive feedback loop. Msi-NPs could self-assemble from polymerized siRNAs targeting Rac1 and p110β together with thiolated glycol chitosan. The combinatory inhibition of Rac1 and p110β successfully inhibited the PI3K signaling pathway in PI3K tumor suppressor phosphatase and tensin homolog (PTEN) deficient prostate cancer cells, resulting in significant delays in cell proliferation and migration. The Msi-NP delivery system can provide an alternative therapeutic strategy to overcome the challenges in PI3K inhibitor monotherapy.