The bearing capacity of offshore single pile composite foundations can be significantly affected by the spatially variable soil properties and the different soil layers installing the pile. The previous research mainly focuses on effects of isotropy or transverse anisotropy spatial variable soil on the bearing capacity and failure mechanism of piles embedded in a single soil layer. The practical sites generally contain multiple soil layers and the soil properties may exhibit strong rotated anisotropy characteristics due to the complex geological movements. However, how the rotated anisotropy spatial variability of soil property affects the bearing capacity of the offshore single pile composite foundation embedded into multiple soil layers remains unclear. This study aims to systematically investigate the effects of rotated anisotropy three-dimensional spatial variability of soil properties on the vertical bearing capacity of the offshore single pile composite foundation embedded into two soil layers. The three-dimensional random finite element is used to simulate the pile-soil response of the offshore single pile composite foundations under vertical static loads. The influence of the scale of fluctuation delta, rotated angle of anisotropy, and coefficient of variation of different soil parameters including elastic modulus E, cohesion c, and internal friction angle phi are investigated. The results show that the COV of E and c have a larger influence than that of phi. The rotated anisotropy of the upper-layer soil generally has a prominent effect on the bearing capacity of the pile compared with the lower-layer soil especially when the horizontal scale of fluctuation is large. These findings underscore the importance of accounting for rotated anisotropy spatial variability in the design of offshore single pile composite foundations.