Nanothermometers are emerging probes as biomedical diagnostic tools. Especially appealing are nanoprobes using NIR light in the range of biological transparency window (BTW) since they have the advantages of a deeper penetration into biological tissues, better contrast, reduced phototoxicity and photobleaching. This article reports the preparation and characterization of organic nanoparticles (ONPs) doped with two polychlorinated trityl radicals (TTM and PTM), as well as studies of their electronic and optical properties. Such ONPs having inside isolated radical molecules and dimeric excimers, can be two-photon excited showing optimal properties for temperature sensing. Remarkably, in TTM-based ONPs the emission intensity of the isolated radical species is unaltered increasing temperature, while the excimer emission intensity decreases strongly being thereby able to monitor temperature changes with an excellent thermal absolute sensitivity of 0.6-3.7%K-1 in the temperature range of 278-328K. The temperature dependence of the excimeric bands of ONPs are theoretically simulated by using electronic structure calculations and a vibronic Hamiltonian model. Finally, TTM-doped ONPs as ratiometric NIR-nanothermometers are tested with two-photon excitationwith enucleated pig eye sclera, as a real tissue model, obtaining a similar temperature sensitivity as in aqueous suspensions, demonstrating their potential as NIR nanothermometers for bio applications.