Here a double-side multiple partial exposure (DoMPE) method is proposed to fabricate an embedded SU-8 microstructure with more flexible inside cross section. The proposed method uses standard lithography equipment and needs only single-layer coating of negative photoresist SU-8 on glass substrate without bonding process. Process parameters, including development thickness at different front and back-side partial exposure doses, are experimentally characterized. Reflection effect due to Cr layer on glass substrate is shown to have influence on the development depth of SU-8 in front partial exposure. It is found that coating thicker SU-8 not only can reduce reflection effect, but also can attenuate cross-link effect due to exposure dose accumulation on SU-8 from both front and back sides. Finally, an embedded SU-8 microstructure is demonstrated to verify that the proposed DoMPE method needs only single-layer SU-8 coating to fabricate not just embedded microstructures, but also embedded microstructure with asymmetric inside cross section.