Tabular data have been playing a mostly important role in diverse real-world fields, such as healthcare, engineering, finance, etc.With the recent success of deep learning, many tabular machine learning (ML) methods based on deep networks (e.g., Transformer, ResNet) have achieved competitive performance on tabular benchmarks. However, existing deep tabular ML methods suffer from the representation entanglement and localization, which largely hinders their prediction performance and leads to performance inconsistency on tabular tasks.To overcome these problems, we explore a novel direction of applying prototype learning for tabular ML and propose a prototype-based tabular representation learning framework, PTaRL, for tabular prediction tasks. The core idea of PTaRL is to construct prototype-based projection space (P-Space) and learn the disentangled representation around global data prototypes. Specifically, PTaRL mainly involves two stages: (i) Prototype Generating, that constructs global prototypes as the basis vectors of P-Space for representation, and (ii) Prototype Projecting, that projects the data samples into P-Space and keeps the core global data information via Optimal Transport. Then, to further acquire the disentangled representations, we constrain PTaRL with two strategies: (i) to diversify the coordinates towards global prototypes of different representations within P-Space, we bring up a diversifying constraint for representation calibration; (ii) to avoid prototype entanglement in P-Space, we introduce a matrix orthogonalization constraint to ensure the independence of global prototypes. Finally, we conduct extensive experiments in PTaRL coupled with state-of-the-art deep tabular ML models on various tabular benchmarks and the results have shown our consistent superiority.