The novel phenomena arising from Bose-Einstein condensates with spatially and spatiotemporally modulated nonlinearities in external potential is reviewed from a theoretical viewpoint. We first present theoretical analysis and numerical studies of the localized nonlinear matter waves in one-dimensional single and two-component BECs with spatially and spatiotemporally modulated nonlinearities, respectively. It is shown that the spatially or spatiotemporally modulated nonlinearity can support stable novel localized nonlinear matter waves such as the breathing solitons and moving solitons. Then the quasi-two-dimensional BEC with spatially modulated nonlinearity is investigated and we show that all of the BECs, similar to the linear harmonic oscillator, can have an arbitrary number of localized nonlinear matter waves with discrete energies. Their properties are determined by the principal quantum number and secondary quantum number. Moreover, we investigate the quantized vortices in a rotating BEC with spatiotemporally modulated interaction in harmonic and anharmonic potentials, respectively. The exact quantized vortex and giant vortex solutions are constructed explicitly by similarity transformation. Their stability behavior is examined by numerical simulation, which shows that a new series of stable vortex states which are defined by radial and angular quantum numbers, can be supported by the spatiotemporally modulated interaction in this system. We find that there exist stable quantized vortices with large topological charges in repulsive condensates with spatiotemporally modulated interaction.