Ageing is a universal decline of physiological functions accompanied by an increase in risks of developing morbidity, diseases, and death. Calorie restriction (CR) without malnutrition has been shown to improve lifespan from simple model organisms to mammals, and extensive research over the past decades have identified several universally conserved signalling pathways by which CR regulates lifespan. More recently, emerging evidence has suggested that modulation of intake levels of macronutrients and micronutrients can also impact healthspan and lifespan in model organisms. These findings propose potentially promising and cost-effective approaches to promote healthy ageing and longevity in humans through personalised nutrition. In this review, we summarise the mechanisms by which CR promotes healthspan and longevity, focusing on the mitochondrial reactive oxygen species (ROS) and several universally conserved geroprotective nutrient-sensing pathways (insulin/insulin-like growth factor (IGF-1), AMP-activated protein kinase (AMPK), mTOR). We further discuss the accumulating data supporting that changes in dietary pattern, levels of nutrient intake (both macronutrient and micronutrient) and functional foods can impact healthspan through acting on the key components of nutrient-sensing and immunoprotective pathways, providing fundamental support for future research and development of anti-ageing diets and dietary regimes.