Extracellular matrix (ECM) is a three-dimensional network of macromolecules that provides a microenvironment capable of supporting and regulating cell functions. However, only few research organisms are available for the systematic dissection of the composition and functions of the ECM, particularly during regeneration. We utilized a free-living flatworm Schmidtea mediterranea to develop an integrative approach consisting of decellularization, proteomics, and RNA-interference (RNAi) to characterize and investigate ECM functions during tissue homeostasis and regeneration. High-quality ECM was isolated from planarians, and its matrisome profile was characterized by LC-MS/MS. The functions of identified ECM components were interrogated using RNAi. Using this approach, we discovered that heparan sulfate proteoglycan and kyphoscoliosis peptidase are essential for both tissue homeostasis and regeneration. Altogether, our strategy provides a robust experimental approach for identifying novel ECM components involved in regeneration that might not be discovered bioinformatically.