Acetylcholine (ACh) and noradrenaline (NA) are major neuromodulators that play key roles in modulating sensory cortical processing. However, it is unclear whether cholinergic neurons in the basal forebrain (BF) and noradrenergic neurons in the locus coeruleus (LC) project to and modulate specific sensory cortex in a modality-specific manner. Here we mapped BF and LC projections to different sensory cortices by dual retrograde tracing. We found that most of cholinergic neurons innervate distinct sensory cortex with high levels of modality selectivity. On the other hand, a substantial number of noradrenergic neurons show diverging projections into multiple sensory cortices. Consistent with these anatomical features, optogenetic activation of cholinergic neurons in BF sub-nuclei induces modality-selective desynchronization in a specific sensory cortex, whereas activation of LC noradrenergic neurons induces broad desynchronization throughout multiple sensory cortices. Our findings demonstrate clear distinction in the circuit organization and function of BF cholinergic and LC noradrenergic inputs into sensory cortical areas.