Ef7 controls rice heading date. In the present study, an allele of Ef7, Ef7-l, was cloned from the indica rice cultivar Longtefu. Sequence analysis indicated that Ef7-l is a novel Ef7 allele and there are five amino acid substitutions in Ef7-l compared with its wild type from Nipponbare. Based on the sequence variation between Ef7-l and Ef7, we developed a near-isogenic line (NIL) CL63 with the background of japonica Nipponbare via marker-assisted selection. The heading date of the NIL CL63 was postponed for approximate six days under long day (LD) condition compared with Nipponbare. In short day (SD) condition, there was no obvious difference in heading date between Nipponbare and CL63. Under the natural field at Yangzhou, the novel allele Ef7-l could result in significant increase of plant height and grain weight in CL63 compared with Nipponbare. The qRT-PCR analysis revealed that there was not significant difference in Ef7 gene expression level between Nipponbare and CL63 under both LD and SD conditions. But the Ef7-l allele could affect rice heading date by up-regulating the expression level of OsPHYB gene under LD condition.