A method and an apparatus for coded focal stack photographing are provided. The method includes: changing a focal surface within a single exposure time and per-pixel coding a sensor readout for each focal surface to obtain a modulation function M(y,z), where y⊂{y1,y2} is a two-dimensional spatial coordinate and z is a depth coordinate of a latent three-dimensional focal stack F(y,z); coding the latent three-dimensional focal stack F(y,z) into a two-dimensional sensor image I(y) by using the modulation function M(y,z); and achieving one or more of a programmable non-planar focal surface imaging, an interleaved focal stack imaging, and a compressive focal stack imaging, based on the modulation functions M(y,z) and the two-dimensional sensor image I(y).