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Creep behavior is a very important attribute of shale and is crucial in the design of hydraulic fracturing schemes to ensure the long-term stable development of shale gas. However, how different shale minerals, organic matter, bedding planes, and pores affect the micro-creep behavior of Upper Ordovician Wufeng and Lower Silurian Longmaxi (WF–LMX) Formation shales is poorly understood. In this study, we employed a nanoindentation mechanical testing technique alongside rock mineralogical, major elemental, and pore analyses to investigate the creep behavior and influencing factors of WF–LMX shales at the microscale. The results show that (1) the creep displacement (Δh) and indentation creep parameter (CIT) are each positively correlated with clay, total pore volume, and clay + total organic carbon (TOC) contents but negatively correlated with the content of quartz, excess SiO2, and TOC. We found weak or no correlation between the occurrence of minor rock constituents, such as feldspar, carbonates, and pyrite, and the shale creep properties; (2) the creep parameters (Δh, CIT, and stress exponent (n)) exhibit anisotropy due to the layering of shale, with values 7.3%–24.2% higher in the plane perpendicular to bedding (X1) than those in the plane parallel to bedding (X3). The creep displacement exhibits negative correlations with Young's modulus, hardness, and stress exponent (n), especially for the X1 direction; (3) compared with those of China's Yanchang shale, the stress exponents of WF–LMX shale are relatively high (8.5–30), indicating that the average creep capacity of WF–LMX shale is relatively weak. Overall, nanoindentation technology has shown great potential in studying shale creep and provides quantitative data support for macroscopic shale creep research.