To develop perennial rice varieties and realize one planting (year) more harvest planting pattern of increasing yield and farmer's income is one of the most cost-effective strategy involved in safeguarding China's grain supply. In this study, construction and analysis of molecular maps of perennial rice was performed to elucidate the genetic laws of microsatellite loci in perennial Chinese rice, two half-sib F2 populations derived from two perennial Chinese japonica rice (HN2# and CB7#) crossed to the annual indica rice XieqingzaoB (XQZB) were developed to construct two half-sib linkage maps. We established linkage map lengths of 2,036.10 cM and 1,878.23 cM with average genetic distance of 18.85 cM and 17.23 cM by using 108 and 109 SSR markers in both HN2# and CB7# map, respectively. Chi-square value (χ2) for genotypes in the F2 populations of both HN2# and CB7# were 134.85 and 291.02, respectively, and exhibited extreme significant bias towards XQZB. χ2 value for genotype on each linkage group of both HN2# and CB7# map ranged from 2.23 to 175.67, from 4.53 to 191.52, respectively. Genotypes on linkage groups of both the 1st, 2nd, 3rd, 4th, 6th, 8th, 9th, 10th, and 12th in HN2# map and 1st, 2nd, 3rd, 5th, 6th, 7th, 9th, 11th, and 12th in CB7# map deviated from the Mendelian ratio. There 38 F2 individual in HN2# and 47 F2 individual in CB7# population deviated from the Mendelian ratio, respectively. Altogether 32 markers showed segregation distortion (29.63%) and clustered on the 3rd, 4th and 6th of linkage in HN2# map, there 44 markers showed segregation distortion (40.37%) and clustered on the 3rd, 5th, 6th, 7th, 9th, and 12th of linkage in CB7# map. Overall, this study lays a good foundation for the mining of beneficial genes and the innovation and utilization of perennial Chinese rice genetic resources.