Ichnofossils are well developed in clastic rock reservoirs in marine and transitional facies, which can considerably change the physical properties of the reservoir. However, this influence is not well understood, raising an important problem in the effective development of petroleum reservoirs. This paper analyzes continental shelf margin delta reservoirs through core observation, cast thin section observation and reservoir physical property test. Some important scientific insights are obtained: (1) The presence of Cruziana ichnofacies, including Asterosoma, Ophiomorpha, Planolites, Skolithos, Thalassinoides, and other ichnofossils can be used to identify in subaqueous distributary channels, subaqueous levee, frontal sheet sand, abandoned river channels, crevasse channels, main channels and channel mouth bars. Considerable differences in the types of ichnofossils and the degree of bioturbation can be observed in the different petrofacies. (2) Ichnofossils and bioturbation play a complex role in controlling reservoir properties. The reservoir physical properties have the characteristics of a decrease–increase–decrease curve with increasing bioturbation degree. This complex change is controlled by the sediment mixing and packing of bioturbation and the diagenetic environment controlled by the ichnofossils. (3) Sea-level cycle changes affect the modification of the reservoir through sediment packing. Bioturbation weakens the reservoir’s physical property when sea level slowly rises and improves the reservoir’s physical property when base level slowly falls.