The design of ratiometric probes for imaging of carbon monoxide (CO) in subcellular organelles is critical to elucidate its biological and pathological functions. In this work, we establish a ratiometric fluorescent probe (Mito-NIB-CO) for imaging of CO in mitochondria. The mitochondria-targeting unit (triphenylphosphonium moiety) and CO-responsive unit (allyl ether moiety) are covalently linking into the single molecule (Mito-NIB-CO) to achieve the multifunctional effect. Upon being treated with CO, Mito-NIB-CO underwent the cleavage of allyl ether element in the presence of PdCl₂, resulting in the structural and spectral conversion. This characteristic afforded Mito-NIB-CO to be a ratiometric probe for CO with two fluorescent emission bands. Additionally, the probe Mito-NIB-CO exhibited other distinct merits, including preeminent selectivity and sensitivity. What’s more, profiting from triphenylphosphonium moiety, the probe Mito-NIB-CO can specifically target the mitochondria and realize quantitative detection of exogenous/endogenous CO in mitochondria.