Matched molecular pair analysis (MMPA) is a tool to extract knowledge of medicinal chemistry from existing experimental data, and it relates changes in activities or properties to specific structural changes. More recently, MMPA has also been applied in multi-objective optimization and de novo drug design. Here, we discuss the concept, techniques, and case studies of MMPA, which provide an overview of the current development in the field of MMPA. This Perspective also summarizes up-to-date MMPA applications and highlights the successes and opportunities for further MMPA advances.