Reservoir alteration of crude oils is ubiquitous in petroleum reservoirs. Alteration can change the composition and physicochemical properties of crude oils, and complicate oil-source correlations and origin studies of crude oils. Thus, the identification and assessment of reservoir alteration could provide a better understanding of the formation and evolution of crude oils. In this study, the effects of reservoir alteration (e.g., biodegradation, gas washing, water washing, and mixing) on oils in the Junggar Basin, northwest China, were identified and assessed by combining diamondoid indices with other commonly studied crude oil properties. The results indicate that: (1) diamondoid indices can be used to evaluate the intensity of reservoir alteration on oils (e.g., slight biodegradation and water washing has no effect on diamondoids; moderate biodegradation and water washing can result in a marked increase in diamondoid concentrations; severe biodegradation and water washing significantly changes diamondoid concentration and isomerization ratios); (2) diamondoid indices can assist in determining the type of reservoir alteration of oils (e.g., condensate formed by gas washing has a lower diamondoid concentration than that generated by thermal cracking; differing from biodegradation and water washing, gas washing can affect diamondoid ratios; mixing can be identified by a combination of diamondoid concentrations and other parameters, such as API gravity and biomarker indices in oils). Therefore, diamondoids provide specific information as to the reservoir alteration of oils, which is useful in further understanding of the origin and evolution of crude oils in the Junggar Basin.