Development of multicolor-emitting upconversion nanoparticles (UCNPs) is of significant importance for applications in optical encoding, anti-counterfeiting, display, and bioimaging. However, realizing the orthogonal three-primary color (TPC) upconversion luminescence in a single nanoparticle remains a huge challenge. Herein, we have rationally designed core-multishell-structured NaYF4 UCNPs through regulating the dopant concentration, composition of luminescent layers, and shell position and thickness, which are capable of emitting red, green, and blue luminescence with high color purity in response to ternary near-infrared quadrature excitations (1560/808/980 nm). Moreover, their high color purity is well retained with varying excitation power densities. This orthogonal TPC emissions property of such UCNPs endows them with great promise in the field of security. As a proof-of-concept, we have demonstrated the feasibility of combining such UCNPs with MnO2 nanosheets for information encryption and decryption. This work not only offers a new way to achieve TPC upconversion luminescence at a single nanoparticle level but also broadens the scope of application for security protection.