The functional relationship between bone and cartilage is modulated by mechanical factors. Scarce data exist on the relationship between bone shape and the spatial distribution of cartilage thickness. This study has three aims: first, to characterise the coupled variation in knee bone morphology and cartilage thickness distributions in knees with healthy cartilage. The second aim was to investigate this relationship as a function of sex, height, body mass, and age. The third aim was to characterise the morphological differences between males and females. MR images of 51 adult knees (28.4±4.1 years) were obtained from a previous study and used to train a statistical shape model of the femur, tibia, and patella and their cartilages. Five linear regression models were fitted to characterise morphology as a function of sex, height, body mass, and age. A logistic regression classifier was fitted to characterise morphological differences between males and females, and 10-fold cross-validation was performed to evaluate the models’ performance. Our results showed that cartilage thickness and its distribution was coupled to bone morphology, including both size (mode 1) and shape variations (mode 2 onwards). The first three shape modes captured over 90% of the variance and described the overall size, diaphysis size, femoral shaft angle, and corresponding changes to the spatial distribution of the cartilages. These modes were sex-linked (p < .0001, p < .05, p < .01, for modes 1, 2, and 3 respectively) and could classify sex with an accuracy of 94.1% (95% CI [83.8%, 98.8%]). Height was a predictor of joint size (p <. 0001) and diaphysis size (p < .05). Body mass was a predictor of joint size (p < .1) and femoral shaft angle (p < .1). Age was not correlated with any of the modes. This study demonstrated the coupled relationship between bone and cartilage, showing that cartilage is thicker with increased bone size, diaphysis size, and decreased femoral shaft angle. Our findings show that sexual dimorphism is strong in these first three modes, and that bone shape and cartilage thickness at the joint are strongly correlated with height but weakly correlated with mass.