Maternal gut microbiota is thought to be one of the important factors in the developmental origins of health and disease (DOHaD) concept, but the effects of maternal gut microbiota on foetal growth are not well known. In this study, the association between maternal gut microbiota and foetal growth was investigated. Maternal and newborn information, as well as stool samples at the third trimester of pregnancy, were obtained from 51 mother–newborn pairs from the Chiba study of Mother and Child Health (C-MACH). Gut microbiota was analysed by 16S rRNA sequencing of stool samples and short-chain fatty acids (SCFAs) in stool were analysed by gas chromatography-tandem mass spectrometry. After adjustment for covariates, it was found that maternal gut microbial diversity had a positive association with head circumference in newborn males (Chao 1: adjusted r = 0.515, p = 0.029). Genus Parabacteroides and genus Eggerthella showed negative associations with newborn head circumference and weight, respectively in males (genus Parabacteroides: adjusted r = −0.598, p = 0.009, genus Eggerthella: adjusted r = −0.481, p = 0.043). On the other hand, genus Streptococcus showed a negative association with newborn height in females (adjusted r = −0.413, p = 0.040). In addition, hexanoate was involved in the association between maternal gut microbiota and newborn anthropometrics in the univariate analysis, but not in the multivariate analysis. These data suggest that maternal gut microbiota has sex-specific effects on foetal growth. Maternal gut microbiota is an important factor for optimal intrauterine growth.