Organic agriculture is of great socioeconomic significance because it can promote the nutritional quality of horticultural crops and is environmentally friendly. However, owing to the lack of techniques for studying complex aroma-related chemical profiles, limited information is available on the influence of organic practices on the flavor quality of strawberries, one of the primary factors driving consumer preferences. Here, two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC-TOF-MS) and flavoromics analysis was employed to investigate the profiles and differences in the volatile organic compounds (VOCs) of strawberries under organic (without imidacloprid) and conventional (with imidacloprid) agricultural practices. A total of 1164 VOCs, representing 23 chemical classes (e.g., aldehydes, terpenes, and furanone compounds), were detected, which is the highest number of VOCs that have ever been detected in strawberries. The sensory evaluation results indicated that there was a notable influence of imidacloprid (IMI) on the aroma of the strawberries. Principal component analysis and partial least squares discriminant analysis results suggested that the composition of volatile compounds significantly differed in the present study between the IMI-treated and non-IMI-treated groups. Furthermore, the flavor-related indicators of 25 key contributors to the differences between the two treatment groups suggested that VOC profiles can be considered an indicator for distinguishing between strawberries from different agricultural practices. Flavoromics can provide new insights into the quality of strawberries from different agricultural practices.