In this paper, based on microfluidic systems, we propose a DNA algorithm for solving the special 0-1 integer programming problem, which has n variables and m constraint terms. In our method, capillary electrophoresis (CE) is used to transfer and separate DNA strands, and the solutions are distinguished by analyzing the fluorescence imaging obtained by laser-induced fluorescence (LIF). Under the control of CE workstation, DNA strands with different lengths are separated and transferred according to an advanced program. This method has advantages such as low cost, low error, short operation time, and simple experimental steps. Moreover, there is no need to reconstruct probes and the size of biochip is linearly increased with the complexity of the problem.