In order to assign the tolerances of focusing optical systems automatically, the tolerance allocation module is developed as a component of the optical simulation software OTS, and the tolerances of optical elements are optimized by this module. Based on the optical transmission matrix and the linear model of tolerance, the merit function, tolerance allocation and feedback are explored. The reasonable tolerances are assigned by Monte Carlo method and other numerical techniques. An adaptive optimization algorithm is proposed and implemented in the software according to the sensitivity of every element, and verified by a multielement bi-pass experimental optical system. The advantage of the algorithm is shown in examples that the average number of iteration is decreased by 2 loops, and the total runtime is 40% less than Zemax with the similar results. This analysis is valuable for manufacturing and assembling optical systems.