Fine particulate matter (PM2.5), which is known to impact public health, has received widespread attention recently. However, the long-term impact of maternal PM2.5 exposure remains unclear. To illuminate whether maternal PM2.5 exposure can affect serum lipoproteins and intestinal flora of offspring, mice received PM2.5 by intratracheal instillation during gestation and lactation. On postnatal day (PND) 35, serum lipoproteins of male and female pups were measured. Additionally, gut microbiota of offspring on PND 3, 10, 21 and 35 were measured by 16S rDNA sequencing of the colon contents. A higher serum triglyceride (TG) concentration in male offspring was observed in the exposed PM2.5 group (p < 0.05) compared with the control group, while there was no significant difference in lipoproteins for female offspring. On PND 35, Bacteroides, Desulfovibrio, and Anaerotruncus were enriched in the male offspring of the PM2.5-exposed group, and the control group had an increased abundance of Streptococcus. However, for female offspring on PND35, Clostridium XI was found to be enriched in the control group. A positive correlation between Bacteroides and serum TG concentration (r = 0.47, p = 0.02) was determined by Spearman's correlation analysis. These results suggest that serum TG and gut microbiota of offspring could be influenced by maternal PM2.5 exposure in a sex-specific manner. Abnormal lipid metabolism might be relevant to the changes of gut microbiota.