Applying the orthogonal principle for distinguishable second near-infrared (NIR-II) emissions has brought new dimensions for ratio fluorescence imaging (RFI) detection and information encryption, deepening the tissue detection depth and improving signal-to-noise ratio and information security. However, the orthogonal NIR-II emissions underlying these advanced optical applications have been reported only in heterogeneous structures and mixtures, limiting their practicality and potential impact. Herein, NIR-I-activated orthogonal NIR-IIb/c (1530/1825nm) emissions nanoparticles (ONNPs) are developed by spatially separated doping of Tm3+ and Er3+ emitter upon switching 808 and 980nm excitations. RFI techniques and orthogonal NIR-II emission ONNPs are used to demonstrate vessel depth detection based on wavelength-dependent optical attenuation properties in tissue. The superiority of the optical coding and encoding process in a 4×1 binary matrix is demonstrated for anticounterfeiting and decryption imaging of quick-response (QR) code for information storage. The research progress of this NIR-II orthogonal emissions probe will drive the development of biomedical sensing, imaging safety, and future biophotonics technologies.