The food environment has been determined to affect a range of healthy eating and health indicators, but the study on the regional difference of food environment effects on these outcomes is limited. This study aimed to examine whether food environment factors influence vegetable and fruit acquisition and healthy eating behaviors in urban and rural areas using a nationwide dataset. The study participants were community-dwelling older adults aged 65 years and older (n = 830) who participated in the 2019 Consumer Behavior Survey for Food provided by the Korea Rural Economic Institute. Food environment factors were assessed using questionnaires measuring perceived food accessibility and affordability. The negative perceptions of food environment were related to lower vegetable and fruit acquisitions and poor healthy eating behaviors. The higher risks of low vegetable and fruit acquisitions in older rural adults were related to a negative perception of food accessibility only (odds ratio [OR]: 2.34, 95% confidence interval [CI]: 1.27-4.32 for vegetable; OR: 1.96, 95% CI: 1.02-3.75 for fruit). For older urban adults, negative perceptions of both food accessibility and food affordability were related to the increased risk of low vegetable acquisition (OR: 2.03, 95% CI: 1.07-3.83 for food accessibility; OR: 2.52, 95% CI: 1.26-5.04 for food affordability). In terms of healthy eating behaviors, for those who perceived that either food accessibility or affordability was poor, older urban adults were less likely to have various and healthy food eating behaviors when they had a negative perception of affordability (OR: 0.47, 95% CI: 0.25-0.90 for variety; OR: 0.23, 95% CI: 0.11-0.46 for eating healthy foods); however, older rural adults were less likely to have the behaviors when they had a negative perception of accessibility (OR: 0.49, 95% CI: 0.21-0.97 for variety; OR: 0.28, 95% CI: 0.13-0.63 for eating healthy foods). In conclusion, the negative perceptions of food accessibility and affordability were related to low vegetable acquisition and poor healthy eating behaviors. The effects of food accessibility and affordability on vegetable and fruit acquisitions and healthy eating behaviors were different between urban and rural areas.