The research field in enzyme-based biotechnology urgently requires the discovery of new materials and methods with high-performance. Here we report that highly crystalline graphite dots (GDs) can modulate enzyme activities, and simultaneously allow for real-time measurements on enzyme kinetics in combination with mass spectrometry (MS). A well-defined modulation of lipolytic activities from inhibition to enhancement can be realized by selectively coupling lipase enzymes with GDs containing specific functional groups on the surface. As a unique feature of our approach, GDs in the enzyme reaction can simultaneously serve as a versatile matrix for rapid and sensitive detection of the residual enzyme substrate, the intermediate or final product of lipolytic digestion using MS technology. Therefore, enzyme kinetic data can be collected in a real-time, high-throughput format. This work provides a new platform for enzymological research in hybrid bio-catalytic processes with advanced nanotechnology.