Conventional geochemical approaches were utilized in the quantitative prediction of the proportions of mixed-source crude oils derived from the Es3 and Es4 members of the Paleogene Shahejie Formation. The mixed-source oils are accumulated in the middle interval of the Es3 member (Es3M) in the Niuzhuang Sag, which is one of the sags where subtle traps are primarily of lenticular basin-floor turbidite sands within mudstones mostly developed in the Dongying Depression, Bohai Bay Basin. The result showed that about 18–92% of the mixed-source oils were derived from the Es4 source rocks with an average of 55–60%. Reservoirs associated with deep faults appear to have much more Es4 genetic affinity oils. A high proportion of the Es4-derived oils discovered in the Es3M subtle lithological traps in the Niuzhuang Sag have long migration distances. This suggests that surrounding source rocks might not necessarily control the hydrocarbon supply for subtle traps. Subtle migration pathway may play an important role in the vertical oil migration. The traditional concept of hydrocarbons accumulation in these lenticular turbidite sandstone traps within a short migration distance from the surrounding source rocks is not supported by this study. The present result is also consistent with our previous findings that immature oils in the Bamianhe Oilfield in the south slope of the Niuzhuang Sag were actually mixed-source oils mostly sourced from the Es4 in the depocenter of the Niuzhuang Sag, and the petroleum potential of the Es4 member in the Dongying Depression should therefore be re-evaluated.