The stability of Bose-Einstein condensates (BECs) loaded into a two-dimensional shallow harmonic potential well is studied. By using the variational method, the ground state properties for interacting BECs in the shallow trap are discussed. It is shown that the possible stable bound state can exist. The depth of the shallow well plays an important role in stabilizing the BECs.The stability of BECs in the shallow trap with the periodic modulating of atom interaction by using the Feshbach resonance is also discussed. The results show that the collapse and diffusion of BECs in a shallow trap can be controlled by the temporal modulation of the scattering length.