In quantum mechanics, a norm squared wave function can be interpreted as the probability density that describes the likelihood of a particle to be measured in a given position or momentum. This statistical property is at the core of the microcosmos. Meanwhile, machine learning inverse design of materials raised intensive attention, resulting in various intelligent systems for matter engineering. Here, inspired by quantum theory, we propose a probabilistic deep learning paradigm for the inverse design of functional meta-structures. Our probability-density-based neural network (PDN) can accurately capture all plausible meta-structures to meet the desired performances. Local maxima in probability density distribution correspond to the most likely candidates. We verify this approach by designing multiple meta-structures for each targeted transmission spectrum to enrich design choices.