Sago starch is an important carbohydrate resource with a potential relevance for future food security. Flavor characteristics of sago starch play a critical role in product acceptability. To date, the influence of the milling grade and contribution of varietal differences of raw materials on its flavor characteristics, which are produced using similar processing methods, has not been sufficiently explored. In this study, we investigated the effects of varietal differences and milling grades on the sensory and metabolites profile of sago starch samples produced from two different sago varieties that have morphological differences, Tuni variety (Metroxylon rumphii) (spiny) and Molat variety (Metroxylon sagu Rottb.) (spinless), and three different milling process: local grade (milled using rotary shifter 100 mesh size), consumer grade (milled using rotary shifter 120 mesh size) and export grade (milled using vibrating screen 120 mesh size). The analyses were performed through integrated metabolomics and sensory quantitative descriptive analysis. Under similar production methods, varietal differences exerted a stronger influence than the milling grade on both the sensory and metabolite profiles of sago starch samples. Non-volatile metabolites were largely unaffected by the milling grade, whereas volatile compounds exhibited greater sensitivity to milling differences. Partial least squares regression analysis further revealed that sugars and specific volatile metabolites contributed to desirable and off-flavor characteristics between the two varieties. Overall, these findings provide the preliminary insight that varietal differences are the primary determinants of the flavor characteristics of sago starch, rather than milling grades, when the sago starch samples are produced using similar processing methods.