To date, investigations of soils in Shanghai have mainly focused on upper clays, namely, Layer 2–6, generally within 30–40 m depth. Knowledge of the deep clays of Layer 8 and 10, at depths of approximately 50 m and 100 m, respectively, is very limited. In this study, the detailed geotechnical properties of the deep Shanghai clays of these two layers were investigated through a series of field and laboratory tests. Physical property tests showed that both clays can be classified as low-plasticity silty clay. For the first time in Shanghai, high-quality intact clay samples were retrieved from the deep soil using a double-tube rotary sampler. High-pressure oedometer tests and consolidated undrained (CU) triaxial tests were conducted to evaluate the compressibility and shear strength of intact samples. The oedometer tests indicate that Layer 8 is an overconsolidated clay with an overconsolidation ratio (OCR) of 2–3, and Layer 10 is a normally consolidated clay with a light degree of structure. CU triaxial tests further confirmed the above findings. The compressibility of the Layer 8 clay is lower, and its undrained shear strength and effective friction angle are larger than those of Layer 10, with the latter being deeper. The sensitivity framework, based on Burland's intrinsic compression line (ICL) and sedimentary compression line (SCL), can be used to characterize the overconsolidation/structure nature of the deep Shanghai clays. The strain energy method was found to be more suitable than the Casagrande method for determining the preconsolidation pressure of the deep Shanghai clays.