The SDF Merger is a cross-platform, simple tool designed to efficiently merge Structure-Data File (SDF) files. SDF files are widely used in cheminformatics, computational chemistry, and drug discovery research. SDF files store molecular structures with their properties. Researchers used SDF files for diverse workflows such as virtual screening, molecular docking, and high-throughput compound testing. For molecular docking needs, used large number of ligand files which can be SDF files. Managing this large number of SDF files manually is time-consuming and chance to errors. Therefore, creating an SDF merger tool is required for a reliable and accessible use. This tool provides two interfaces such as a desktop application and a webpage interface. The desktop application, built using Python, Tkinter, and RDKit. These support research-intensive workflows, multiple processing of SDF files, and detailed logging. The web application, implemented in pure JavaScript, HTML, and CSS that requires no installation and processes files entirely client-side, ensuring data privacy while providing immediate, drag-and-drop accessibility. Both the desktop and web interface required no installation. The web interface is already live on the GitHub page, and the desktop application as an .exe file is available for download from the SourceForge site. Users can use any of the platforms as per their needs and requirements. The aim of this tool is to solve the complexity of merging SDF file for research purposes. By bridging the gap, SDF Merger uses SDF file management, making it accessible to researchers without programming expertise. Its cross-platform availability, such as a Windows executable and a browser-based web interface, ensures broad usability in academic and educational settings. The tool tried to compute research workflows and reduce technical barriers for users across diverse research environments.