利用第一性原理计算及相关数值模拟及模型分析，致力于凝聚态物理中的多维度磁性中自旋电子学和量子自旋态的理论研究。主要集中在能够用于量子计算、量子调控的分子磁性材料以及可用于存储元件的拓扑磁性材料。研究领域还涉足：反铁磁体、离子输运、二维材料、多铁、拓扑材料以及碳纳米管等。
预言了一类具有强垂直磁各向异性的二维磁性薄膜并发现了高温无序磁结构中的拓扑非平庸性，阐明了反铁磁半导体MnTe零磁场面内各向异性的霍尔效应以及多种分子磁体中多铁性的产生机制。相关成果发表SCI期刊论文12篇，其中第一作者（含共同）包括Physical Review Letters 2篇，Science Advances 1篇等顶级期刊论文，并有一项专利。
J.-X. Yu, D.-T. Chen, J. Gu, J. Chen, J. Jiang, L. Zhang, Y. Yu, X.-G. Zhang, V. S. Zapf, and H.-P. Cheng, "Three Jahn-Teller States of Matter in Spin-Crossover System Mn(taa)". Phys. Rev. Lett. 124, 227201 (2020)
J.-X. Yu, G. Christou, and H.-P. Cheng, "Analysis of exchange interactions in dimers of Mn3 single-molecule magnets, and their sensitivity to external pressure". J. Phys. Chem. C 124, 14768 (2020)
M. Yazback, J.-X. Yu, S. Liu, L. Zhang, N. S. Sullivan, and H.-P. Cheng, "First-Principles study of an S = 1 quasi-1D quantum molecular magnetic material". Phys. Rev. B 103, 054434 (2021)
G. Yin, J.-X. Yu (equal contribution), Y. Liu, R. K. Lake, J. Zang and K. L. Wang, "Planar Hall Effect in Antiferromagnetic MnTe Thin Films". Phys. Rev. Lett. 122, 106602 (2019)
J.-X. Yu, M. Daly and J. Zang, "Thermally driven topology in frustrated systems".Phys. Rev. B 99, 104431 (2019)