Abstract We report the generation of multiple electron beams using a cold atom electron source (CAES) combined with a spatial light modulator (SLM). In the experiment, neutral 87Rb atoms are confined in a magneto-optical trap and cooled to approximately 700μK. By shaping the intensity profile of the excitation laser via the SLM, the spatial distribution of the excited atoms can be precisely controlled. The excited atoms are then ionized by a dye laser, and the ionized electrons are extracted and focused by an electric field to form multiple electron beams. As a demonstration, we generate regular arrays of 3×3,4×4,5×5,6×6 beams, each with a spot size of about 100μm and a normalized transverse emittance of ∼0.4×10−9m⋅rad⋅eV. This programmable electron beam technique holds potential for applications in electron-beam lithography and wafer inspection.