SummaryMonitoring and localizing molecules on living plants is critical for understanding their growth, development and disease. However, current techniques for molecular imaging of living plants often lack spatial information or require tedious pre‐labelling. Here, we proposed a novel molecular imaging platform that combines sliver nanowire‐doped Ti3C2 MXene (Ag NWs@MXene) flexible film substrate with laser desorption/ionization mass spectrometry imaging (AMF‐LDI‐MSI) to study the spatial distribution of biomolecules on the surface of living plants. This platform overcomes the MSI challenges posed by difficult‐to‐slice plant tissues (e.g., tough or water‐rich roots and fragile flowers) and enables precisely transfer and visualize the molecule. Comparisons of the measurement results to those from matrix‐assisted LDI‐MSI (MALDI‐MSI) technology demonstrate the accuracy and reliability of the platform. Biocompatibility evaluations indicated that the platform without observable adverse effects on the health of living plants. The distribution of growth and disease‐associated signalling molecules, such as choline, organic acids and carbohydrates, can be in situ non‐destructively detected on the surfaces of living plants, which is important for tracking the health of plants and their diseased areas. AMF‐LDI‐MSI platform can serve as a promising tool for label‐free, in situ and non‐destructive monitoring of functional biomolecules and plant growth from a spatial perspective.