The effects of hydrothermal treatment (soaking, cooking, and a combination of soaking and cooking) on free phenolics (FPs) and insoluble bound phenolics (IBPs) metabolites of both parboiled and non-parboiled rice were investigated using multivariate analysis, pathway analysis, and correlation heatmaps. A lowering in phenolic acids was recorded for both rice samples after the hydrothermal treatments. Both parboiled and non-parboiled rice possessed significant amounts of (−) epicatechin and kaempferol in the forms of FPs and IBPs. Total phenol contents (7.38–40.59 mg/100g) and total flavonoid contents (1.46–6.34 mg/100 g) were found to be higher in IBs form in parboiled rice. DPPH radical scavenging activity (52.7–222 μmol TE/g) and reducing power (287–566 μmol TE/g) were also found to be higher in IBPs in parboiled rice. The PLS-DA and VIP scores multivariate analyses demonstrated the complex behavior of phenolic metabolites in hydrothermally treated rice. A strong association (0.61≤r ≤ 0.97) among total phenol, total flavonoid, and antioxidant activity suggests their possible contribution to antioxidant behavior. Results indicated that cooking in combination with soaking resulted in higher TPC, TFC, and antioxidant activity than regular cooking, which would have the potential to be a healthy choice for consumers.