The kinetics of forming multifunctional nanostructures, such as nanotheranostic superstructures, is often highly protracted, involving macroscopic time scales and resulting in nanostructures that correspond to kinetically stable states rather than thermodynamic equilibrium. Predicting such kinetically stable nanostructures becomes a great challenge due to the widely different, relevant time scales that are implicated in the formation kinetics of nano-objects. We develop a methodology, integral of first-passage times from constrained simulations (IFS), to predict kinetically stable, planet−satellite nanotheranostic superstructures. The simulation results are consistent with our experimental observations. The developed methodology enables the exploration of time scales from molecular vibrations of 10 −3 ns toward macroscopic scales, 10 10 ns, which permits the rational design and prediction of kinetically stable nanotheranostic superstructures for applications in nanomedicine.