In this study, the biological characteristics and breeding applicability of five indica-compatible japonica germplasm (Minghui413, Minghui1616, Minghui1707, Minghui512 and Minghui 509) have been studied, which will provide theoretical reference for the future breeding of indica-compatible japonica germplasm and the heterosis utilization of the indica-japonica inter-subspecific hybrids. Five germplasm showed longer growth period, moderate plant height, erect panicle type, small panicle, dense grain setting, increased effective panicles per plant, high setting percentage and big grain size. The analysis using the Cheng’s indexes showed that Minghui413, Minghui1616, Minghui1707 and Minghui512 belonged to japonicalinous, while Minghui509 belonged to japonica. In addition, these germplasm showed a good indica compatibility. For instance, the seed setting rate of F1 by crossing with the two-line indica sterile line was >75% with a highest value of 89.80%. These germplasm are able to restore the fertility of indica CMS lines (WA type, YS type, and K type), and the seed setting rate was >80%. Moreover, the flag leaves of the five germplasm accessions could maintain a higher photosynthetic rate in the later period of growth and breeding, beneficial to the filling and fullness of grains. Except DSH (Duration from seeding to heading), plant height and 1000-grain weight, the heterosis of five indica-compatible japonica germplasms showed competitive performance in panicle length, effective panicle per plant, total grain number per panicle, seed setting rate, number of primary branch rachis and number of secondary branch rachis per panicle. Among them, panicle length, primary branch rachis number, secondary branch rachis number and total grain number per panicle all showed more than 10% competitive advantage. Indica-japonica hybrid rice Hualiangyou3716 and Huanliangyou3707, developed from two-line indica sterile line Hua1037S and the indica-compatible japonica germplasms Minghui1616 and Minghui1707 were registered and released by Fujian Provincial Crop Variety Appraisal Committee. The yield production of these two varieties was significantly higher than that of the control. Therefore, this study reported the five indica-compatible japonica germplasm accessions, which showed good indica compatibility and broad restoring spectrum with a good prospect in the subspecies heterosis utilization.