Natural product-originated carbon dots represent a charming and valuable platform for bio-fluorescence probes; however, the application scope of these probes is seriously restricted, due to the indistinct molecular structures of these bio-probes and the inaccurate interactions between the probe and detected guest molecule. Herein, a novel strategy of keto–enol tautomerism-mediated quinone aromatization has been achieved for Cochineal bio-based quinone carbon dot synthesis. Then, a photo-induced intermolecular cross-redox reaction was accomplished with tetracycline for quinone carbon dot molecule transformation and fluorescence change. This work represents a pioneer for intermolecular interaction simulation and bonding energy evaluation of carbon dots for trace organics detection.