Recently, a novel bootstrap method for numerical calculations in matrix models and quantum mechanical systems is proposed. We apply the method to certain quantum mechanical systems derived from some well-known local toric Calabi-Yau geometries, where the exact quantization conditions have been conjecturally related to topological string theory. We find that the bootstrap method provides a promising alternative for the precision numerical calculations of the energy eigenvalues. An improvement in our approach is to use a larger set of two-dimensional operators instead of one-dimensional ones. We also apply our improved bootstrap methods to some non-relativistic models in the recent literature and demonstrate better numerical accuracies.