Whole wheat bread (WWB) is strongly recommended to replace regular white bread (RWB) in daily diet, while its undesirable sensory characteristics hinder its widespread consumption. Herein, a combination of sourdough fermentation and an innovative compound improver was developed to improve the baking performance of WWB. The results demonstrated that the specific volume, crumb structure, and texture of the improved whole wheat bread (IWWB) were remarkably superior to WWB and comparable to RWB. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) showed that the gluten network of WWB was disrupted by fibers, while IWWB presented a cross-linked gluten network. Fourier transform infrared (FTIR) spectroscopy analysis revealed that the contents of ordered and elastic secondary structures in IWWB gluten protein were significantly higher than those in WWB. Moreover, compared with WWB and RWB, IWWB exhibited markedly stronger antioxidant activities, lower estimated glycemic index, and slower staling rate. Overall, IWWB displayed excellent sensory, nutritional, and antistaling properties, which would satisfy consumers' demands for both deliciousness and nutrition. The potential mechanisms of quality improvement revealed in this study may be enlightening for the development of other functional bread aimed at balancing the nutrition and sensory quality.