The invention provides a colony selecting throughout improving method, which is applied to a colony selector so as to shorten a selecting path of a probe module and to subsequently improve a selecting throughout; the colony selecting throughout improving method is characterized by comprising the following steps: 1, establishing a mathematical model of the selecting path; 2, sequentially distributing colony numbers and probe numbers, so that an initial chromosome is obtained, and obtaining an initial population in a mode of random insertion; 3, conducting an iterative operation; 4, repeating the step 3 until iteration times reach preset times, so that a final population is obtained; and 5, selecting a chromosome, which has the maximum fitted value, from the final population and outputting the selected chromosome as a result, so that the colony selector can conduct colony selecting in accordance with colony and probe matching in the result. With the application of the colony selecting throughout improving method provided by the invention, the probe module of the colony selector can be optimized, so that the moving path of the probe module is shortened in a selecting course and subsequently the colony selecting throughout is improved.