This study presents a comprehensive three-dimensional finite element modeling and parametric analysis of composite beam-to-column joints in steel–timber composite structures. The investigation encompassed a variety of shear connector configurations, end plate designs, and bolt dimensions, aiming to elucidate their respective influences on the structural performance and behavior of these joints. Through meticulous numerical simulation, this research sought to enhance the understanding of the interactions and load transfer mechanisms within composite connections, thereby contributing to the optimization of design practices in the field of structural engineering. The load–displacement relationship for timber–steel composite joints subjected to monotonic loading was investigated using ABAQUS 6.14 software. This study systematically analyzed the effects of various parameters, including different configurations of shear connectors, end plate thicknesses, and bolt dimensions, on the overall performance of the joints. Through this comprehensive numerical analysis, the research aimed to provide deeper insights into the mechanical behavior and structural integrity of these composite connections under the applied loading conditions. A non-linear finite element model of timber was developed and verified with the results of the experiment in this study. The findings are discussed in detail, highlighting the intricate relationships between the selected parameters and their respective effects on the performance and overall stability of the composite connections. This thorough evaluation aimed to enhance the understanding of how these variables interact within the context of composite joint design and behavior. Finally, design recommendations for composite structures, such as the dimensions of the bolt, end plate thickness, and different sizes of shear connectors are provided.