Abstract In recent decades, the application of organic fertilizer to agricultural soils has attracted wide attention. However, few studies have carefully explored the effects of humic acid fertilizer on soil temperature, radiation, and the physiology of plant leaves, especially when coupled with different irrigation methods. To provide a better growing environment for crops and explore the best regulation method of humic acid fertilizer and irrigation in the farmland soil environment on the Songnen Plain, China, through field experiments, we selected rice as the test crop and applied humic acid fertilizer to the soil with different irrigation methods. The effects of different humic acid fertilizers and irrigation methods on the soil temperature and radiation changes during different growth stages were examined, and the subtle differences in agronomic and fluorescence characteristics in different growth stages of rice plants were compared. The results showed that the soil temperature was not significantly different among all the treatments. However, radiation interception was obviously different, and the best value was observed in the CT5 treatment. The fluorescence indices and leaf chlorophyll relative content ( SPAD ) differed with the change in humic acid fertilizer application and irrigation methods. At the jointing and heading stages, the F v /F m values of the CT5, FT5 and WT5 treatments were larger than those of the other treatments, and the best value was recorded in the CT5 treatment. The differences in NPQ at these two stages were significant, and the NPQ in the CT5 treatment was significantly higher than that in the other treatments ( P < 0.05). In general, the Q P under control irrigation was greater than that under flood and wet irrigation ( P < 0.05). Moreover, there were no significant differences among the gradients under the different humic acid fertilizer application methods in terms of Q P ( P > 0.05). Additionally, SPAD values were higher under the CT5 and FT5 treatments.