Measuring the conformations of protein and protein-ligand complexes in solution is critical for investigating protein bioactivities, but their rapid analyses remain as challenging problems. Here, we report the coupling of Taylor dispersion analysis (TDA) with mass spectrometry (MS) for the rapid conformation differentiation of protein and noncovalent protein complex in solution environments. First, a branched capillary design was applied to achieve double band detection for the peak retention time correction in TDA measurements. After ionization, analytes were further detected and distinguished by their mass to charge (m/z) ratios in the consequent MS analysis. As a result, protein or protein complex in a mixture could be analyzed in terms of both hydrodynamic radius and m/z. The feasibility of this method was verified by analyzing a mixture of angiotensin II and phenylalanine, and the conformations of cytochrome C at different pH conditions were then investigated. As proof-of-concept demonstrations, the complexes of tri-N-acetylchitotriose with two proteins (lysozyme and cytochrome C) were characterized with results verified by molecular dynamics simulations. The TDA-MS method is promising for rapid structural analyses of trace amounts protein-ligand complexes, which could potentially be used to differentiate intact protein or protein complex conformations.