Concentrations of toxic chemicals in mothers highly correlate with those in their children; moreover, the levels are higher in children than in mothers. Non-persistent chemicals with a short half-life including phthalate metabolites, bisphenol A (BPA), triclosan (TCS), and parabens are metabolized and excreted through urine. Therefore, we assessed the urine concentrations of phthalate metabolites, BPA, TCS, and parabens; correlated the concentrations with exposure levels; and assessed the within-individual variability of these chemicals in mothers and their infants. We collected 225 and 71 samples from 45 mothers and 36 infants, respectively. For the variability analysis, 189 and 42 samples were collected from nine mothers and their infants, respectively. The median concentrations of phthalate metabolites in the mothers and infants were 0.53–26.2 and 0.81–61.8 μg/L, respectively, and those of BPA, TCS, and parabens were 0.24–76.3 and 2.06–12.5 μg/L, respectively. The concentrations of monoethyl phthalate (MEP), mono-N-butyl phthalate (MnBP), mono-isobutyl phthalate (MiBP), and BPA in the mothers were positively correlated with those in infants (0.45, 0.62, and 0.89, respectively; p < 0.05), whereas toxic chemical concentrations in infants were higher than those in the mothers. With respect to the within-individual intraclass correlation coefficient (ICC), the first morning void (FMV) of the mothers had high ICCs for all chemicals (range: 0.72–0.99), except for BPA, monobenzyl phthalate (MBzP), and monocarboxyoctyl phthalate (MCOP). The ICC values of most chemicals were moderate to high (range: 0.34–0.99) in the first morning void. However, there were different patterns of ICCs in the infants. These findings indicate the importance of mother–infant pair studies and the necessity of research in infants, as they have different exposure sources and pathways from adults.