Petroleum contamination remains a worldwide issue requiring cost-effective bioremediation techniques. However, establishing a universal bioremediation strategy for all types of oil-polluted sites is challenging. This difficulty arises from the heterogeneity of soil textures, the complexity of oil products, and the variations in local climate and environment across different oil-contaminated regions. Several factors can impede bioremediation efficacy: (i) differences in bioavailability and biodegradability between aliphatic and aromatic fractions of crude oil; (ii) inconsistencies between hydrocarbon removal efficiency and toxicity attenuation during remediation; (iii) varying adverse effect of aliphatic and aromatic fractions on soil microorganisms. This review examines the ecotoxicity risk of petroleum contamination to soil fauna and flora. It also discusses three primary bioremediation strategies: biostimulation with nutrients, bioaugmentation with petroleum degraders, and phytoremediation with plants. Based on current research and state-of-the-art challenges, we highlighted future research scopes should focus on (i) exploring the ecotoxicity differentiation of aliphatic and aromatic fractions of crude oil, (ii) establishing unified risk factors and indicators for evaluating oil pollution toxicity, (iii) determining the fate and transformation of aliphatic and aromatic fractions of crude oil using advanced analytical techniques, and (iv) developing combined bioremediation techniques that improve petroleum removal and ecotoxicity attenuation.