The optimal design of clonal seed orchard was carried out to determine a more reasonable ratio of clones, so as to avoid self-crossing and inbreeding between clones, and ensure the consistency of florescence of clones in seed orchard as far as possible, in order to promote effective parental pollination, improve seed yield and quality, and provide reference for the design of highgeneration seed orchard. The genetic distance between the parents of Pinus sylvestris var. mongolica Litv. in the National Production Base of Improved Seeds in Honghua’erji of Inner Mongolia Autonomous Region was determined by using SSR markers and Gene Marker V2.2 software. Florescence and pollen range were set, and 13 clones were randomly selected as experimental data. The twopopulation improved adaptive step-length fruit fly optimization algorithm (TIASFOA) was designed, and improved fruit fly optimization algorithm (IFOA), particle swarm optimization (PSO) and genetic algorithm (GA) were compared and analyzed in three aspects: fitness value, convergence and the number of clones with adjacent or identical flowering period in pollination range. Under genetic distance, flowering and pollen counts were known, the population size of 20~60 was carried out 200 times respectively, the average, maximum, minimum and variance fitness values of TIASFOA were smaller than those of IFOA, PSO and GA. When the population size was 20, the mean value of the sum of number of clones in the same or adjacent florescence of TIASFOA was 125 and 204, respectively, which was larger than that of the other three algorithms. In this population size, TIASFOA can obtain the optimal fitness value of 133.016, which was 0.283 different from the minimum value of 132.733 when the population size was 50. Genetic distance, flowering period and pollen quantity were taken as constraints for optimal calculation, which were closer to the production environment and provided references for the optimal design of clonal seed orchard. In practical application, population scale of 20 can be used to obtain better seed orchard schemes in a short time and maintain the high genetic diversity of seed orchard. 