The Transformer model, renowned for its powerful attention mechanism, has achieved state-of-the-art performance in various artificial intelligence tasks but faces challenges with quantum data. With a growing focus on leveraging quantum machine learning for quantum data, particularly in quantum chemistry, we propose the Molecular Quantum Transformer (MQT) for modeling interactions in molecular quantum systems. By utilizing quantum circuits to implement the attention mechanism on the molecular configurations, MQT can efficiently calculate ground-state energies for all configurations. Numerical demonstrations show that in calculating ground-state energies for H2, LiH, BeH2, and H4, MQT outperforms the classical Transformer, highlighting the promise of quantum effects in Transformer structures. Furthermore, its pretraining capability on diverse molecular data facilitates the efficient learning of new molecules, extending its applicability to complex molecular systems with minimal additional effort. Our method offers an alternative to existing quantum algorithms for estimating ground-state energies, opening new avenues in quantum chemistry and materials science.