Modelling multiscale systems from nanoscale to macroscale requires the use of atomistic and continuum methods and, correspondingly, different computer codes. Here, we develop a seamless method based on DeepONet, which is a composite deep neural network (a branch and a trunk network) for regressing operators. In particular, we consider bubble growth dynamics, and we model tiny bubbles of initial size from 100 nm to 10 in the atomistic regime. After an offline training based on data from both regimes, DeepONet can make accurate predictions of bubble growth on-the-fly (within a fraction of a second) across four orders of magnitude difference in spatial scales and two orders of magnitude in temporal scales. The framework of DeepONet is general and can be used for unifying physical models of different scales in diverse multiscale applications.