With the improvement of health awareness, low-sugar and gluten-free baked foods have become a research hotspot for special dietary populations. Traditional cookies are mostly made of wheat flour and sucrose, which pose risks of gluten allergy and a high estimated glycemic index(eGI). Research on the synergistic application of composite flour and a single natural high-potency sweetener in cookies remains limited. To develop a healthy cookie suitable for gluten-intolerant individuals and sugar-conscious consumers, this study completely replaced wheat flour with a blend of buckwheat flour and tapioca starch, and substituted sucrose with mogroside. This study systematically explored the optimal processing parameters for low-sugar, gluten-free buckwheat cookies. Using sensory scores as the evaluation index, single-factor and response surface methodology were employed to investigate the effects of blending ratio, mogroside addition, and baking time on cookie quality. The texture, flavor, and in vitro digestive properties of the optimized product were further analyzed. The optimal processing parameters were determined as follows: Buckwheat flour: tapioca starch = 1:0.6 (by weight), mogroside addition of 0.15% (based on flour weight), and baking time of 15 min. The resulting cookies exhibited uniform color, crispy texture, moderate sweetness, and a sensory score of 89. Compared with the control cookies, the product showed significantly lower springiness and gumminess, richer flavor compounds, and an eGI value of only 33.73, classified as a low-eGI food. The combination of composite flour and mogroside can produce gluten-free cookies with good sensory quality and low eGI. This study provides a theoretical basis for the development of low-sugar, gluten-free cookies.