Heading date is a factor closely associated with grain yield in rice (Oryza sativa L). In recent decades, a number of genes responsible for heading time have been identified, the variation of which contributes to the expansion of the rice cultivation area. However, it is difficult to compare the phenotypic effects of these genes due to the different genetic backgrounds. In this study, we generated 14 heading time mutants using CRISPR/Cas9 gene-editing technology and marker-assisted selection with a japonica Sasanishiki wild-type (WT) genetic background. Photoperiod sensitivity, the relationship between days to heading (DTH), and yield components of mutants were investigated. We found that the yield increases with increases in DTH, but eventually plateaus at maximum and then began to decrease, whereas the biomass continued to increase. The mutants exerted distinctly different effects on DTH and yield components. The convergent double mutants had severe yield reduction compared with single mutants, even with a DTH that was similar to that of single mutants. We also found that an elite mutant of se14 achieved a yield equal to that of the WT, but with heading occurring 10 days earlier. A sequence analysis of 72 cultivars collected from the japonica cultivated zone shows that elite se14 mutants have not been applied to rice breeding. Our study demonstrates the effect of heading time genes on reproductive transition and yield components under an identical genetic background. These results may provide new insights into rice breeding using heading time mutants.