Flow lithography in a conventional rectangular microchannel is limited to fabrication of particles for which only the shapes of top perimeters are controlled. We present a flow lithography technique for fabrication of microparticles of diverse 3D shapes and multiple layers using non-rectangular microchannels with designed cross sections that allow the creation of complex shapes and diverse cross-sectional shapes. Variations in cross-sectional shape allow high-throughput, on-demand production of microparticles in unconventional shapes such as tetrahedrons and pyramids. Multilayered 3D particles weregenerated in an enlarging triangular channel combined with on-chip PDMS valves, which allow particle alignment and fluid exchange. These 3D microparticles are expected to further expand the wide varietyof applications of microparticles, especially in drug delivery and tissue engineering fields.