Appropriate preference for light or dark is crucial for animal survival. However, the underlying neural circuit mechanism remains unclear especially for vertebrates. Here, integrating behavioral assay, in vivo opto- and electro-physiological recordings, optogenetics and morphological tracing in larval zebrafish, we found that a circuitry consisting of retinal ganglion cells (RGCs), eminentia thalamus (EmT) and left dorsal Habenula (L-dHb) mediates light preference behavior. Lesion or dysfunction of the L-dHb diminished retina-dependent light preference, while optogenetic activation of the L-dHb endowed eye-removing zebrafish with light preference. L-dHb neurons can code background luminance, because they exhibit sustained and light intensity-dependent responses to light flashes as long as stimuli last, a property important for light preference behavior. Light preference-associated visual inputs of the L-dHb are conveyed through EmT neurons, which contact the axonal arborization field 4 of RGCs, display sustained light responses, project to the L-dHb, form excitatory synapses with L-dHb neurons, and are required for light preference. Thus, our study identifies a neural circuitry, which underlies light preference in vertebrates, and provides new insights about the function of the EmT and Habenula.