Red blood cells play an essential role in the immune system. Moreover, red blood cell count (RBC) is an important clinical indicator of various diseases, including anemia, type 2 diabetes and the metabolic syndrome. Thus, it is necessary to reveal the genetic mechanism of RBC for animal disease resistance breeding. However, quite a few studies had focused on porcine RBC, especially at different stages. Thus, studies on porcine RBC at different stages are needed for disease resistant breeding. In this study, the porcine RBC of 20-, 33-, and 80-day old were measured, and genetic parameter estimation and genome-wide association study (GWAS) were both performed. As a result, the heritability was about 0.6 at the early stages, much higher than that at 80 days. Nine novel genome wide significant single nucleotide polymorphisms (SNPs), located at Sus scrofa chromosome (SSC)3, 4, 8, 9, 10 and 15, respectively, were identified. Further, TGFβ2, TMCC2 and PPP1R15B genes were identified as important candidate genes of porcine red blood cell count. So different SNPs and candidate genes were found significantly associated with porcine RBC at different stages, suggesting that different genes might play key roles on porcine RBC at different stages. Overall, new evidences were offered in this study for the genetic bases of animal RBC, and that the SNPs and candidate genes would be useful for disease resistant breeding of pig.