An analytical technique for residual sodium chlorate and nonanoic acid is proposed in this work to investigate the ranges of residue amounts in field-collected samples of red beans as well as the degradation of the compounds during storage conditions. The background value of endogenous nonanoic acid in red beans is also explored to provide evidence for verification of organic agricultural products or implementation of incentive measures for natural drying programs. In pretreatment, samples of sodium chlorate and nonanoic acid were extracted after oscillation via deionized water and acetone/n-hexane for corresponding ion chromatography (IC) and gas chromatography–mass spectrometry (GC-MS) analysis. The limit of quantification (LOQ) was determined to be 0.5 µg/g for sodium chlorate and 0.05 µg/g for nonanoic acid, and the results of the recovery tests for both substances conformed to the performance requirements of the standard methods. After drying the test sample for 5 days, red bean pods (including both kernels and capsules) were detected to have > 50 µg/g sodium chlorate and > 6 µg/g nonanoic acid, and no degradation trend was found in the concentration of sodium chlorate or nonanoic acid during the 3 weeks when the samples were kept in an outdoor sunlight or indoor cold storage environment. Based on the nonanoic acid concentration range in 78 field samples, the average endogenous nweonanoic acid content in red bean pods was calculated to be 1.4 g/g and did not exceed 1.88 g/g at the 99.9% confidence level, the allowable value for nonanoic acid is thus 2 g/g.