In neuroscience, it’s one of the central goals to decipher neuronal ensembles’ function in the neural circuits. Recently, the progress of probes for optogenetic actuators and calcium indicators afford the probability for simultaneous optical manipulation and imaging of neuronal ensembles. Although with point-scanning imaging and localized optical stimulation, previous work had achieved all-optical interrogation of neural circuits in the local brain areas of mice and zebrafish larvae, no attempt was made to optical interrogate neuronal ensembles’ function across the whole-brain. Here, we combined the fast volumetric imaging technique, light-sheet microscopy which was an order of magnitude faster than the point-scanning method, with digital laser beam shaping device, digital micromirror device (DMD), to learn about neuronal activities across the whole brain of behaving larval zebrafish. Using the spectrally separated calcium indicator, GCaMP6f, and activity actuator, ChrimsonR, we can simultaneously image and manipulate neuronal ensembles with minimal spectral cross-talk. Besides, to monitor the behavior of zebrafish larvae, a high-speed camera was introduced into the system. To demonstrate the system’s function, arbitrarily selected neurons was stimulated during the whole-brain neuronal activities’ imaging, which effectively activated the synaptic connections and brain-wide downstream neural circuits and evoked stereotyped behaviors. These results demonstrate the system’s ability in studying the function of brain-wide neuronal ensembles in small animals.