Speech brain-computer interfaces (speech BCIs), which convert brain signals into spoken words or sentences, have demonstrated great potential for high-performance BCI communication. Phonemes are the basic pronunciation units. For monosyllabic languages such as Chinese Mandarin, where a word usually contains less than three phonemes, accurate decoding of phonemes plays a vital role. We found that in the neural representation space, phonemes with similar pronunciations are often inseparable, leading to confusion in phoneme classification. We mapped the neural signals of phoneme pronunciation into a hyperbolic space for a more distinct phoneme representation. Critically, we proposed a hyperbolic hierarchical clustering approach to specifically learn a phoneme-level structure to guide the representation. We found such representation facilitated greater distance between similar phonemes, effectively reducing confusion. In the phoneme decoding task, our approach demonstrated an average accuracy of 75.21% for 21 phonemes and outperformed existing methods across different experimental days. Our approach showed high accuracy in phoneme classification. By learning the phoneme-level neural structure, the representations of neural signals were more discriminative and interpretable. Our approach can potentially facilitate high-performance speech BCIs for Chinese and other monosyllabic languages.