2A97 is the third-generation aluminum-lithium (Al-Li) alloy developed by China. However, the fine equiaxed zone (FEQZ) of weld is the weakest area of its joint, which severely limits its practical application in the aerospace field. In this study, the macro- and microscopic characteristics of weld and the formation mechanism of the microstructure under the condition of non-autogenous laser welding (NLW) were investigated. The results showed that the droplet transition behavior varied with the change in the content of low-boiling-temperature elements of filler metals. The porosity imperfection in 2A97-T3 via NLW was relatively serious, which could be modified by using ER2319 filler metal. The addition of Zr in the equiaxed zone resulted in effective refinement of the equiaxed dendrite. Furthermore, it also led to the alternate distribution of coarse and fine equiaxed dendrites. The distribution of FEQZ was affected by the flow of the weld pool and concentrated at the four corners of the weld. Moreover, its morphology and distribution ranges were influenced significantly by the welding parameters and filler metals.