Objective: To determine the effects of naturally derived probiotic strains individually or combination on a short‐term diet‐induced obesity model. Design and Methods: C57BL/6J mice ( n = 50) were randomly divided into five groups, then fed a high‐fat high‐cholesterol diet (HFCD), HFCD and Lactobacillus plantarum KY1032 (PL, 10 10 cfu/day), HFCD and Lactobacillus curvatus HY7601 (CU, 10 10 cfu/day), HFCD and in combination with PL+CU (10 10 cfu/day), or a normal diet (ND) for 9 weeks. Results: PL and CU showed distinct and shared metabolic activity against a panel of 50 carbohydrates. Fat accumulation in adipose tissue and liver was significantly reduced by probiotic strains CU or PL+CU. Probiotic strains CU or PL+CU reduced cholesterol in plasma and liver, while PL+CL had a synergistic effect on hepatic triglycerides. Probiotic strains PL+CU combination was more effective for inhibiting gene expressions of various fatty acid synthesis enzymes in the liver, concomitant with decreases in fatty acid oxidation‐related enzyme activities and their gene expressions. Conclusions: Multi‐strain probiotics may prove more beneficial than single‐strain probiotics to combat fat accumulation and metabolic alterations in diet‐induced obesity.