Walking environment is commonly cited as an element that reduces the risk of obesity. Many literatures have shown that the impact of walking environment on the incidence rate of obesity may vary across gender, but few studies have conducted in-depth investigations. The present study aimed to provide empirical evidence for a cross-sectional association between the built community environment and the incidence of obesity among male and female residents. Thus, we collected height and weight level of 1355 residents and constructed seven walking environment indicators around 54 communities. Also, BMI was calculated and categorized to define overweight and obesity. We used generalized estimation equation to evaluate the gender-specific association between walking environment on obesity based on a diverse population sample. The study showed that female residents who lived in neighborhoods with higher road sky view index (p = 0.033; OR = 0.002 [95% CI = 0.001–0.619]) and increased intersection density (p = 0.009; OR = 0.979 [95% CI = 0.963–0.995]) showed lower risk of increased BMI, but the advantage does not successfully radiate significant obesity consequences. In addition, the increased density of bus stops can also reduce the risk of obesity in women groups (p = 0.035; OR = 0.910 [95% CI = 0.836–0.990]). These findings suggest that women were more sensitive and were more likely to make different behavioral choices and physiological responses due to distinct walking environments. This provides useful evidence for future obesity prevention and urban planning.