Familial longevity is characterized by beneficial metabolic phenotype in lipid metabolism and APOE genetic variation. Although effects of lipid metabolism and the genetic basis for human longevity remain largely unclear, the contribution of high-density lipoprotein cholesterol (HDL-C) and APOE ε2 allele has been repeatedly demonstrated. This study was designed to determine whether ApoE isoforms and HDL-C levels marked the familial longevity status in an offspring cohort with the age range of 20-89 years old and subsequently to explore the correlation between these two markers and the aging. In the Bama Aging Study (BAS), we recruited 312 offspring from longevity historical families and 298 controls from non-longevity historical families. Information on APOE genotype frequencies, lipid levels, and population characteristics were recorded. No evidence was found to support the association of APOE genotypes with HDL-C and age. HDL-C was significantly higher in longevity group (p < 0.0001). Scatter plot showed a moderately strong linear relationship between the HDL-C level and age in longevity group (r = 0.213, p < 0.001). We conclude that the variation of the APOE gene may not influence familial longevity status at a certain age but the moderate-high HDL-C level contributes to the familial longevity in Bama.