The rice–crayfish continuous production system developed rapidly due to its high economic benefits and eco-friendly nature in China. This study explored the effects of mechanically transplanted methods and planting geometry on the relationship between rice yield and canopy structure, under rice-crayfish rotation using excellent-quality indica rice, and carried out in 2018 and 2019. Three mechanical transplantation methods were set as follows: carpet seedlings mechanically transplanted with 30 cm equal row spacing (CMTE), pot seedlings mechanically transplanted with narrow row spacing with alternating 23 cm/33 cm wide row spacing (PMTWN), and equal row spacing at 28 cm (PMTE). Different plant spacings (CMTE1-CMTE6, PMTWN1-PMTWN6, PMTE3, and PMTE4) were set in accordance with different mechanical transplanting methods. CMTE and PMTWN both included six transplanting densities, while PMTE included 2 transplanting densities. Results showed that rice yield was improved by 2.87–6.59% under PMTWN when compared to CMTE, which was mainly due to the increase in spikelets per panicle and filled-grain percentage. Dry matter accumulation was increased and larger leaf area indexes were observed under PMTWN than CMTE at the rice main growth stage. Yield of CMTE and PMTWN treatments increased at first and then declined with decreased planting density. Under suitable planting density, PMTWN could optimize rice population structure and increase rice yield compared with PMTE. For tested rice variety, pot seedlings were mechanically transplanted alternating alternating 23 cm/33 cm wide row spacing, combined with a plant spacing of 16.8 cm, was proper for its yield improvement under rice-crayfish rotation.