The multi-canopy cropping system is a new way to increase the number of soybeans grown. It is based on the idea of vertical agriculture. Short and tall plants are grown on the same hill in this method. The tall plants form a canopy, so the vertical space can be used to grow crops. The study aimed to determine how breeding programs could be used to create rice varieties for a multi-canopy cropping system. The tests were done in the dry and wet seasons at the Universitas Sumatera Utara in Medan, Indonesia. For plant height, number of leaves, number of branches, and number of pods, the genotype x canopy system interaction effect was significant. Over the two seasons, the average yield of the multi-canopy cropping system was 6.61 t ha−1compared to 5.59 t ha−1for the monoculture. The average yield of seven genotypes in two cropping systems, monoculture and multi-canopy, was 5.59 t ha−1and 6.62 t ha−1. The mean average agronomic traits over monoculture and multi-canopy plant height, number of leaves, number of branches, and number of pods were 67.63 cm, 28.83, 8.00, and the number of pods 154.42. The AMMI analysis shows most of the differences between genotype x environment. The first group is made up of the environment during the dry season and the wet season. The mean net assimilation rate of soybean genotypes under multi-canopy and monoculture systems monoculture and multi-canopy was 1.81 μg cm2d−1and 2.87 μg cm2d−1. The tall and short genotypes in multi-canopy have the highest yield, so they could be used to breed rice varieties that do well in multi-canopy.