Weathered diesel oil (WDO) has less biodegradable and volatile characteristics, and its bioremediation could be a challenge. In this study, the effectiveness of enhanced bioremediation via biopile processes for the cleanup of WDO-contaminated soils was evaluated. Six biopiles were constructed and operated with the following six different amendments addition: red bran (12 kg), water-soluble fertilizer (20 L/week), highly oxygenated water (20 L/d, dissolved oxygen = 25 mg/L), petroleum hydrocarbon-degrading bacterial culture (20 L/week), mixture of the above amendments, and natural attenuation (no amendment). Each biopile contained 5 m3 [2.5 m (L) × 2 m (W) × 1 m (H)] of WDO-contaminated soils [initial total petroleum hydrocarbon (TPH) concentrations = 3015 to 3785 mg/kg]. Soils were mixed with amendments and tilled for air supplement twice a week with soil moisture around 25%. Metagenomics analyses were applied to determine the microbial biodiversity and strains responsible for hydrocarbon biodegradation. Results show that the biopile system with mixed supplements (mixture group) had the highest TPH removal efficiency (79% of TPH removal) followed by red bran addition group with a removal efficiency of approximately 73% during the 42-day operation. The first-order TPH decay rates in mixture and red bran biopiles were around 3.2 × 10−2 1/d, which was 4.8 times higher than that obtained from natural attenuation biopile. Biopiles with red bran and mixture supplements contained carbon substrates and nutrients, which could effectively activate microbial activities and accelerate the TPH biodegradation. High carbon number compounds (C > 20) in WDO could be biodegraded within 24 days in the biopile with mixed amendments. Results from metagenomics study indicate that Sphingomonas and Pseudomonas might cause removal of heavy components (C24–30) and light components of petroleum hydrocarbons (C10–16), respectively.