The research focused on in vivo diagnosis and treatment of metabolic organ diseases is of critical clinical value. Our research team has independently developed and improved upon the technology of photoacoustic microscopy, enabling the development of optical imaging methods with high spatiotemporal resolution for studying organ metabolism. This breakthrough has led to insights into the progression of metabolic diseases in organs such as the liver and kidneys, as well as advancements in optical lipolysis therapies. In this report, we introduce the development and advancements of optical imaging techniques, including photoacoustic tomography, photoacoustic microscopy, and in vivo fluorescence imaging (NIR I/II). We discuss the non-invasive and non-ionizing nature of these techniques in diagnosing metabolic disorders such as metabolic-associated fatty liver disease and metabolic kidney disease. Additionally, we explore the application of this technology in monitoring long-term metabolic therapies for fat reduction. Finally, we showcase the diagnostic applications and future prospects of these techniques in clinical patients.