Activation of the epithelial to mesenchymal transition (EMT) in photodynamic therapy (PDT) can lead to the recurrence and progression of tumors. To enhance the effects of PDT, it is essential to inhibit the Wnt/β-catenin signaling pathway involved in EMT progression. Herein, we used polyethylene glycol-polyethyleneimine-chlorin e6 (PEG-PEI-Ce6) nanoparticles to efficiently deliver Wnt-1 small interfering RNA (siRNA) to the cytoplasm of KB cells (oral squamous cell carcinoma) that were subjected to PDT. Wnt-1 siRNA effectively inhibited the Wnt/β-catenin signaling pathway, reducing the expression of Wnt-1, β-catenin and vimentin that are crucial to the EMT. Combined with Wnt-1 siRNA, PEG-PEI-Ce6 nanoparticle mediated PDT inhibited cell growth and enhanced the cancer cell killing effect remarkably. Our results show the promise of combination therapy of PEG-PEI-Ce6 nanoparticles for delivery of Wnt-1 siRNA along with PDT in the treatment of oral cancer.