Considering the importance of green and secure communications in the complex environments of the future Internet of Things (IoT), a secure wireless powered communication network (WPCN) assisted by double reconfigurable intelligent surfaces (RISs) is investigated. To maximize the system’s secrecy energy efficiency (SEE), we propose a Lagrange dual decomposition combined with double quadratic transformation and Riemannian manifold optimization (LDD-DQT-RMO) algorithm to jointly optimize the resource allocation, transmit and receive beamforming, and phase shifts at RISs. In particular, the DQT-RMO method is employed for the first time to optimize the phase shifts in the wireless information transmission (WIT) phase. Furthermore, an improved low-complexity algorithm is developed to directly obtain closed-form solutions for the phase shifts. Simulation results demonstrate that the proposed LDD-DQT-RMO and its improved algorithm achieve much lower complexity and faster convergence compared to mainstream algorithms. Moreover, the proposed algorithms exhibit superior SEE performance compared to hybrid double-RIS-assisted WPCN systems in multi-antenna and large-scale RIS scenarios.