Recent progress shows that intersecting D-brane models can give rise to much richer phenomenology than people used to think. Puzzles and anomalies in particle physics can be resolved in D-brane models purely by geometrical constructions of the intersecting D-branes. In this talk, I will discuss two classes of D-brane models. One class of the models offers a scenario connecting the hidden sector physics using Stueckelberg U(1)'s. The other class offers a natural explanation of the recent LHCb flavor anomaly.