A novel optimization algorithm along with the mathematical model for dose control parameters in a step and scan lithography, aiming at an optimal match of the throughput, dose accuracy and cost of ownership of deep ultraviolet (DUV) excimer laser simultaneously is proposed. With the help of variable laser repetition frequency and introduction of a new concept called effective number of pulses, the optimization strategy for a given dose in the effective dose range is achieved and the detailed method to calculate values of all the dose control parameters is proposed. The theoretical study and numerical simulation demonstrate that the new algorithm not only maintains the advantages in throughput and dose accuracy of the currently used one, but also overcomes its drawback of not considering the reduction of laser cost of ownership. It is fully expected that the novel algorithm will show its superiority and provide a better application with the further improvement of DUV excimer laser and its dose control technology.