Hydrogen atoms bonded within molecular cavities often undergo tunneling or thermal-transfer processes that play major roles in diverse physical phenomena. Such transfers may or may not entail intermediate states. The existence of such fleeting states is typically determined by indirect means, while their direct visualization has not been achieved, largely because their concentrations under equilibrium conditions are negligible. Here we use density-functional-theory calculations and scanning-tunneling-microscopy (STM) image simulations to predict that, under specially designed nonequilibrium conditions of voltage-enhanced high transfer rates, the cis-intermediate of the two-hydrogen transfer process in metal-free naphthalocyanine molecules adsorbed on Ag(111) surfaces would be visualizable in a composite image of double-C morphology. As guided by the theoretical predictions, at adjusted scanning temperature and bias, STM experiments achieve a direct visualization of the cis-intermediate. This work demonstrates a practical way to directly visualize elusive intermediates, which enhances understanding of the quantum dynamics of hydrogen atoms.