Soybean is a crucial source of oil, protein, and biofuel, necessitating efficient transformation systems for advancing research. Agrobacterium-mediated transformation is currently the primary method used in the soybean transformation industry and scientific research. However, the low efficiency and genotype dependency of this technology leave significant room for improvement. This study aimed to enhance soybean transformation efficiency by generating and validating three reporter vectors (ZsGreen, TdTomato, and Ruby) and using Agrobacterium Auxiliary Solution (AAS) containing Silwet L-77 and hormone mixtures. Our findings demonstrate that AAS significantly improves hairy root transformation rates. Specifically, this combination increased total root and cotyledon transformation efficiencies compared to the control. We also found that larger vectors like Ruby reduced transformation efficiency compared to smaller markers like GFP and RFP. Furthermore, AAS slightly reduced the co-transformation rate of two separate vectors compared to single vector transformations. Additionally, AAS enhanced soybean hypocotyl transformation rates across various varieties, consistently increasing positive root and explant efficiencies. Notably, transformation rates varied significantly between varieties, with Forrest differing from Williams 82 and Dongnong 50. This research highlights the importance of auxiliary agents and vector size in optimizing soybean transformation, providing insights for future advancements in genetic modification and biotechnology.