Family functioning is found to be associated with overweight and obesity in childhood, but its association with maternal obesity risk behaviors is not clear. This study aimed to investigate whether family functioning is associated with maternal obesity risk behaviors and to inform the development of early obesity interventions. A total of 408 first-time mothers at 24–34 weeks of pregnancy were included in the study. They participated in the Healthy Beginnings Trial (HBT) conducted in southwest Sydney, Australia in 2008. An analysis of cross-sectional baseline data was conducted using ordinal logistic regression modeling. Key measures were assessed using the McMaster Family Assessment Device, and self-reported obesity risk behaviors including excessive consumption of soft drinks, fast food, and excessive small screen time. The study found that 30% of the study population had a family functioning score ≥2, indicating unhealthy family functioning. About one-third (36%) of the mothers had more than one obesity risk behavior. Mothers with a family functioning score ≥2 were more likely to have more than one obesity risk behavior (47% vs. 32%, P < 0.05) than mothers with a lower score. The proportion of mothers with a family functioning score ≥2 increased from 22% to 29% to 39% as the number of maternal obesity risk behaviors increased from 0 to 1 to 2 or more, giving an adjusted proportional odds ratio (AOR) of 2.0 (95% confidence interval (CI) 1.3–3.0, P = 0.001). Family functioning is independently associated with the number of maternal obesity risk behaviors after allowing for the effects of maternal age and education. Overweight and obesity interventions should consider addressing family functioning.