The DNA sequence design is a vital step in reducing undesirable biochemical reactions and incorrect computations in successful DNA computing. To this end, many studies had concentrated on how to design higher quality DNA sequences. However, DNA sequences involve some thermodynamic and conflicting conditions, which in turn reflect the evolutionary algorithm process implemented through chemical reactions. In the present study, we applied an improved multi-objective particle swarm optimization (IMOPSO) algorithm to DNA sequence design, in which a chaotic map is combined with this algorithm to avoid falling into local optima. The experimental simulation and statistical results showed that the DNA sequence design method based on IMOPSO has higher reliability than the existing sequence design methods such as traditional evolutionary algorithm, invasive weed algorithm, and specialized methods.