Gel-based DNA separation on microchip will play an important role in future genomic analysis due to its potential for high-efficiency and high-speed. Optimal design of microchip and separation condition is essential to take full advantage of high-speed separation on microchip. Separation length L and electric field strength E, which are crucial for design of microchip system, are focused on in this paper. Simultaneous optimization of L and E was carried out to achieve the most rapid separation. It was shown that the condition of L and E and the shortest separation time is closely related to the shape of resolution Rs surface in a three-dimensional space with axes E, L, and Rs. This surface was investigated, taking sample injection, detector, diffusion, and Joule heating into account. Thermal gradient broadening due to Joule heating helps to produce camber or ridge shape of Rs surface, which is essential for the shortest separation length and separation time. Sample plug length and detection volume should be more carefully controlled in microchip. The property of diffusion coefficient was shown to play a key role in determining Rs surface.