Individual-level analyses have consistently shown associations of travel behaviours with obesity-related measures. However, transport planning policies often target areas rather than individuals. To better inform transport-related policies and initiatives for obesity prevention, area-level relationships need to be investigated. This study linked data from two travel surveys with data from the Australian National Health Survey at the level of Population Health Areas (PHAs) and examined to what extent area-level travel behaviours metrics (prevalence of active travel, mixed travel and sedentary travel, diversity of travel modes) were associated with the rate of high waist circumference. Data from 51,987 travel survey participants were aggregated into 327 PHAs. Bayesian conditional autoregressive models were used to account for spatial autocorrelation. It was found that statistically replacing participants who relied on cars for travel (without walking/cycling) with those engaging in 30+ min/d of walking/cycling (without car use) was associated with a lower rate of high waist circumference. Areas with greater diversity of travel modes (mix of walking/cycling, car use, public transport use) also had lower prevalence of high waist circumference. This data-linkage study suggests that area-level transport planning strategies addressing car dependency, shifting car use to walking/cycling over 30 min/d, may help to reduce obesity.