Hydrogel microparticles are versatile tools for organ modeling due to their simplicity, uniformity, and customizability, yet their limited physiological relevance constrains practical applications. In this study, a heart microparticle model that incorporates endocardial and myocardial structures and functions was developed. Hydrogel microparticles with rough surfaces, embedded with cardiomyocytes, were created using a custom-designed microfluidic device. Surface modification with matrigel enhanced the adhesion and connectivity of endothelial cells, enabling the formation of a densely packed endothelial layer. Real-time analysis, combining microparticle culture with a microfluidic chip-mass spectrometry system, demonstrated the utility of these particles in detecting the cardiotoxicity of heart-related drugs. For example, the analysis revealed that the cardiotoxicity of aconitine and Tie-bang-chui (TBC) was associated with elevated lactate and succinate levels, while processed TBC mitigated this toxicity of TBC by reducing these metabolites. These biomimetic microparticle models provide a novel platform for real-time metabolite analysis and cardiotoxicity research.