Zero‐dimensional boron nitride quantum dots (BNQDs) are arousing interest for their versatile optical, chemical, and biochemical properties. Introducing carbon contents in BNQDs nanostructures is a great challenge to modulate their physicochemical properties. Among the carbon moieties, phenolic groups have attracted attention for their biochemical properties and phenol‐containing nanomaterials are showing great promise for biomedical applications. Herein, the first example of direct synthesis of water dispersible BNQDs exposing phenolic and carboxylic groups is presented. The carbon‐BNQDs are prepared in a single‐step by solvent‐assisted reaction of urea with boronic reagents and are characterized by optical absorption, luminescence, Raman, Fourier transform infrared and NMR spectroscopy, X‐ray photoelectron spectroscopy, dynamic light scattering, and atomic force microscopy. The carbon‐BNQDs exhibit nanodimension, stability, high photothermal conversion efficiency, pH‐responsive luminescence and Z‐potential. The potential of the carbon‐BNQDs to provide photothermal materials in solid by embedding in agarose substrate is successfully investigated. The carbon‐BNQDs exhibit biocompatibility on colorectal adenocarcinoma cells (Caco‐2) and protective effects from chemical and oxidative stress on Caco‐2, osteosarcoma (MG‐63), and microglial (HMC‐3) cells. Amplicon mRNA‐seq analyses for the expression of 56 genes involve in oxidative‐stress and inflammation are performed to evaluate the molecular events responsible for the cell protective effects of the carbon‐BNQDs.