Aim To investigate the possible relationship between variant CD33 rs3865444 and serum lipid levels in long-lived population inhabiting along Hongshuihe River Basin in Guangxi province. Methods Genotyping of CD33 rs3865444 locus was performed by improved multi-temperature ligase detection reaction technique (iMLDR) for long-lived individuals (long-lived group, aged≥90 years, n＝645), non-long-lived elderly (local control group, aged 60～77 years, n＝674) residing in Hongshuihe River Basin and non-long-lived elderly living in Hezhou (non-local control group, aged 60～77 years, n＝662), a town about 600 km from Guangxi Honeshuihe. Association of CD33 rs3865444 genotypes with lipids was analyzed thereafter. Results The frequencies of A allele and its genotype (CA/AA) of females in Hongshuihe River Basin, both long-lived group and long control group, were significantly higher than those of non-local controls; CA/AA genotype of females was higher than that of males in the long-lived group, while this status was opposite between gender in the non-local controls. The levels of TC, LDLC and ApoB of A allele carriers in males in long-lived group were dramatically greater than those of non-A allele carriers (P＜0.0001), while HDLC level of A carriers was lower than non-A carriers in females of local controls; by contrary, HDLC and ApoA levels of females were higher than those of non-A carriers in the non-local controls. Conclusions CD33 rs3865444 polymorphism correlates with lipid levels to some extent, which is influenced by sex and other environmental factors. The enrichment of A allele of CD33 rs3865444 locus in the long-lived females needs further clarification.