High-moisture extrusion (HME) has increasingly garnered attention in the production of plant-based meat analogs. Nevertheless, the disorganized structural properties and poor functional characteristics of HME extrudates pose significant challenges to the advancement of plant-based alternatives in the food industry. The coextrusion of proteins and polysaccharides has emerged as an effective strategy to improve the sensory qualities of HME meat analogs. Herein, we investigated the effects of the type and addition of inulin on the structural and functional properties of HME extrudates comprising soy protein isolate, soy protein concentrate, and wheat protein. The results indicated that inulin facilitated the conversion of 7S to 11S globulin and induced a transformation from a β-turn angle to a β-folded protein structure, promoting lamellar structure formation and enhancing the overall stability of the protein matrix. Optimal results were achieved with the addition of 6% long-chain and short-chain inulin. In terms of functional characteristics, the incorporation of short-chain inulin resulted in a superior fiber structure and protein digestibility, whereas long-chain inulin enhanced the water-holding capacity, rehydration rate, and thermal stability. Additionally, intermolecular interaction analysis revealed that these inulin-induced improvements in the quality of HME extrudates are primarily attributed to the strengthening of disulfide bonds and hydrogen bonds. These findings offer crucial insights for advancing the quality of plant-based meat analogs, providing valuable directions for future product development in the food industry.