Volatile organic compounds (VOCs) are released to the indoor air of retail stores from numerous products and activities, but available literature lacks a systematic understanding of the variability of VOC concentrations. In this study, we measured concentrations of total VOCs (TVOC) in 32 retail stores using a high-sensitivity photoionization detector (PID). Indoor thermal comfort parameters, including temperature, relative humidity, and air velocity, were simultaneously measured using an anemometer. The store-level TVOC concentrations ranged from 30 to 869 ppb and exceeded the LEED guideline in 31 stores. TVOC levels were notably high in hardware stores (median = 536 ppb, p = 0.0002) and paints, household, and home accessories sections within stores (p < 0.05). TVOC levels were elevated in mornings and evenings, possibly due to low ventilation and cleaning activities at the beginning and end of business hours. The between-store, within-store, and temporal variations accounted for 85%, 0.5%, and 14% of the total variance, respectively. The variance structure suggested that in-store VOC concentrations were predominantly driven by their source location, and representative monitoring should first consider covering various store types. Current store VOC levels present health concerns, but further studies are needed to evaluate risks among customers.