研究方向为分子发光分析，研究领域涉及分子荧光光谱法、环境及生物分析、多组分分析、表面分析，特别是各种同步荧光法、低温荧光、导数技术、偏振技术、全内反射荧光、共焦荧光显微等荧光分析新检测原理新技术及应用方面。先后主持包括国家自然科学基金、教育部高等学校骨干教师资助计划项目、教育部优秀青年教师资助计划项目、福建省自然科学基金等的多项科研课题。研制组装了一台具有商品化仪器所不具备的新功能的荧光光谱仪和一台共焦显微荧光系统。已在国内外重要刊物上发表论文70余篇。工作数次被国际上文献称为首次研究、首次报道。更有意义的是，从引用文章看，所提出的分析方法，不仅仅是单纯被引用和评价，而且在国际上还得到了应用。现任期刊《生命科学仪器》编委及中国计量测试学会分析测试质量保证委员会委员。
先后以第一完成者或独立获得厦门大学“嘉庚”奖(1991)；福建省自然科学优秀论文一等奖(1994)；国家教委科技进步三等奖(1997)；厦门大学“清源”科研个人奖(2000)等。
“Surface Plasmon-Coupled Directional Enhanced Raman Scattering by Means of the Reverse Kretschmann Configuration”, Si-Xin Huo, Qian Liu, Shuo-Hui Cao, Wei-Peng Cai, Ling-Yan Meng, Kai-Xin Xie, Yan-Yun Zhai, Cheng Zong, Zhi-Lin Yang, Bin Ren, and Yao-Qun Li*, J.Phys.Chem.Lett. 2015, 6, 2015−2019
“Surface charge modulated aptasensor in a single glass conical nanopore”, Sheng-Lin Cai, Shuo-Hui Cao, Yu-Bin Zheng, Shuang Zhao, Jin-Lei Yang, Yao-Qun Li*, Biosensors and Bioelectronics, 2015, 71, 37–43
“Modulation of surface plasmon coupled emission (SPCE) by a pulsed magnetic field”, Kai-Xin Xie, Shuo-Hui Cao, Qian Liu, Wei-Peng Cai, Si-Xin Huo, Hitoshi Watarai*, and Yao-Qun Li*, Chem. Commun., 2015, 51, 12320-12323
“Label-Free Aptasensor Based on Ultrathin-Linker-Mediated Hot-Spot Assembly to Induce Strong Directional Fluorescence”, Shuo-Hui Cao, Wei-Peng Cai, Qian Liu, Kai-Xin Xie, Yu-Hua Weng, Si-Xin Huo, Zhong-Qun Tian and Yao-Qun Li*, J. Am. Chem. Soc., 2014, 136, 6802−6805.
“Turning on fluorescence by plasmonic assembly with large tunable spacing: a new observation and its biosensing application”, Shuo-Hui Cao, Wei-Peng Cai, Qian Liu, Kai-Xin Xie, Yu-Hua Weng and Yao-Qun Li*, Chem. Commun., 2014, 50, 518-520 (inside cover article)
“Surface Plasmon–Coupled Emission: What Can Directional Fluorescence Bring to Analytical Sciences?”, Shuohui Cao, Weipeng Cai, Qian Liu, Yaoqun Li*, Annu. Rev. of Anal. Chem., 2012, 5, 317-336.
“Electrical, Optical, and Docking Properties of Conical Nanopores”, Yaoqun Li*, Yubin Zheng, Richard N. Zare*, ACS Nano, 2012, 6, 993-997.
“Prism-based Surface Plasmon Coupled Emission Imaging”, Weipeng Cai, Qian Liu, Shuohui Cao, Yuhua Weng, Xiaoqing Liu, Yaoqun Li*, ChemPhysChem, 2012, 13, 3848-3851.
“Dirctional surface plasmon-coupled emission of CdTe quantum dots and its application in Hg sensing”, Xiaoqing Liu, Qian Liu, Shuohui Cao, Weipeng Cai, Yuhua Weng, Kaixin Xie, Yaoqun Li*, Anal. Methods, 2012, 4, 3956-3960. (outside back cover)
“Electric Field Assisted Surface Plasmon-Coupled Directional Emission: An Active Strategy on Enhancing Sensitivity for DNA Sensing and Efficient Discrimination of Single Base Mutation”, Shuohui Cao, Tangtang Xie, Weipeng Cai, Liu, Qian; Yaoqun Li*, J. Am. Chem. Soc., 2011, 133, 1787-1789.
“A novel synchronous fluorescence spectroscopic approach for the rapid determination of three polycyclic aromatic hydrocarbons in tea with simple microwave-assisted pretreatment of sample”, Xiuying Li, Na Li, Hedong Luo, Lirong Lin, Zhexiang Zou, Yuzhu Jia, Yaoqun Li*, J. Agr. Food. Chem., 2011, 59, 5899-5905.
“Smart Homopolymer Modification to Single Glass Conical Nanopore Channels: Dual-stimuli Actuated Highly Efficient Ion-gating”, Lixiang Zhang, Shenglin Cai, Yubin Zheng, Xiaohong Cao, Yaoqun Li*, Adv. Funct. Mater., 2011, 21, 2103-2107.
“Surface plasmon-coupled directional emission based on a conformational-switching signaling aptamer”, Tangtang Xie, Qian Liu, Weipeng Cai, Zhe Chen, Yaoqun Li*, Chem. Commun., 2009, 22, 3190-3192.
中国发明专利：一种食品中苯并(a)芘的荧光快速检测装置，李耀群，邹哲祥，林国春，周娜，李呐，张伟，专利号：ZL200710009900.2，授权日：2011.3.23.
中国发明专利：双模式表面等离子体耦合发射荧光成像检测装置和方法，李耀群，蔡伟鹏，刘倩，曹烁晖，谢凯信，翁玉华，专利号：201310267360.3，授权日2015.10.14