Inorganic elements in crude oil have been used in the reconstruction of the sedimentary environment and oil−oil (source) correlations; however, the effect of biodegradation on these elements has not been investigated sufficiently. In this study, 14 crude oils from the Miaoxi Sag of the Bohai Bay Basin, eastern China, were analyzed using molecular markers, trace elements, and major elements to determine the effect of biodegradation on inorganic elements. The molecular markers indicated that the oils are in the low maturity stage and are derived from similar parent materials in lacustrine source rocks. The high-sulfur oil came from a more reductive and saltier environment compared with the low-sulfur oil. The oils were subjected to varying degrees of biodegradation. The concentrations of Mg, Ca, Mn, Fe, Be, Sc, Rb, Sr, Zr, Pb, Th, and U increased significantly throughout the biodegradation process, while the concentrations of Na, K, Ti, Al, Cr, Zn, Cs, Nb, Ba, Hf, and Tl increased considerably only during the intense biodegradation stage (PM < 4). The concentrations of P, Li, V, Co, Ni, Cu, Ga, Sn, and Ta were not correlated with the level of biodegradation. The V/Ni, V/Co, Ni/Co, Cr/V, Sc/V, and Th/U ratios were affected by biodegradation when PM ≥ 4. Several ratios, including Mg/P, Ca/P, Mn/P, and Fe/P, are proposed as favorable indicators of the level of biodegradation. Differential enrichment of these elements is associated with the effects of organic acids generated by biodegradation on the oil−water−rock interactions in the reservoir.