The abbreviated growth period associated with ratooning, approximately half that of the main season, raises questions about a potential decrease in cadmium (Cd) and arsenic (As) levels in ratoon rice grains. We conducted multi-site field trials with 25 rice varieties spanning two years. Cd levels in ratoon-season rice did not significantly decrease, with some varieties showing a notable increase in Cd levels compared with those in the main season. Some varieties with low Cd accumulation in the main season showed an increase in Cd levels in the ratoon season; however, As levels decreased during the ratoon season for all varieties. Consuming ratoon-season rice could pose increased health risks due to higher Cd levels. Conversely, consuming ratoon-season rice significantly reduced As-related health risks by 3.11–73.87%. Although this decrease in As levels during the ratoon season may provide reassurance, caution should be exercised regarding the potential increase in Cd levels in ratoon-season rice grown in contaminated areas caused by varietal differences, which could lead to elevated health risks. Conclusively, two inbred varieties (XZX45 and ZJZ17) and one hybrid (WLYHZ) variety were identified as suitable for cultivation in mildly to moderately contaminated areas, mitigating the associated health risks.