Greenhouse horticulture (protected cropping) is essential in meeting increasing global food demand under climate change scenarios by ensuring sustainability, efficiency, and productivity. Recent advances in cover materials and photovoltaic technologies have been widely examined in greenhouses to improve light transmission and solar energy capture with promoting energy-saving. We review the studies on advanced greenhouse cover materials with variable light transmittance, the effects of which on leaf photosynthesis, physiology, and yield. We provide insights into the potential key biological processes of crops responding to these light changes, specifically light receptors, signal transduction, nutrient biosynthesis pathways (e.g., carotenoids, antioxidant compounds) during fruit development and ripening. A better understanding of greenhouse cover materials with a focus towards energy-efficient cover materials equipped in greenhouse is an opportunity for better yield and higher nutrient products production in vegetables in response to global climate challenges. Interdisciplinary research on the application of novel cover materials in greenhouses and biological investigation of light-induced physiology and nutrient formation in vegetables may promote yield and health attributes for protected cultivation of vegetables with energy use efficiency.