Breeding rice (Oryza sativa L.) for the multi‐canopy (MC) cropping system is one of the novel ideas for increasing production. This system involves combining rice genotypes with different plant heights to form stratified panicles and flag leaves. This study aimed to elucidate the effects of different characteristics of flag leaves of tall plant genotypes on yield and agronomic traits in MC cultivation. The study was conducted from May 2020 to January 2021 at the IPB University Experimental Station at Babakan, Bogor, West Java, Indonesia. The genetic materials were seven rice inbred lines of F9 from an ongoing breeding program at IPB University, consisting of four tall genotypes with different flag leaf characters, namely IPB187‐F‐90‐1‐1 (ordinary, short flag leaf); IPB189‐F‐19‐2‐1 (V‐shaped, medium‐length flag leaf); IPB187‐F‐40‐1‐2 (V‐shape, narrow, half rolled, and long flag leaf); IPB189‐F‐8‐1‐1 (wide, long flag leaf), and three short genotypes, namely IPB193‐F‐19‐1‐3, IPB187‐F‐69‐2‐3, and IPB189‐F‐13‐1‐1. The experiment was carried out in four environmental conditions, namely: (a) monoculture and (b) MC, 2020 dry season, (c) monoculture, and (d) MC, 2020/2021 wet season, using a randomized complete block design with three replications. The results showed that the genotype × cropping system interaction significantly affected total yield (p < .05). The MC cropping system produced a higher average yield (6.65 t ha–1) than the monoculture (6.01 t ha–1) across the two seasons. The genotype with V‐shape and medium‐length flag leaf gave the highest yield in MC. This study substantiated the potential of breeding rice varieties suitable for the MC system.