The potential of microscale near-infrared spectroscopy (MicroNIR) in determining the dry mixing endpoints of powdered formula and the effects of different nutrient structures on the mixing homogeneity were thoroughly investigated. A MicroNIR spectrometer was installed onto the dry mixing equipment to analyze the formula. The mixing endpoint was calculated using various algorithms, and the accuracy of the endpoint calculation was validated using the national standard method. Furthermore, the impact of nutrient structures on the dry-mixing homogeneity at the microscopic level was examined using optical and scanning electron microscopy. Spectral differences between raw materials and additives in formula are the most prominent in the 1 093~1 285 nm and 1 459~1 645 nm wavelength range, and homogeneous mixing is achieved at 32 min, 48 s. During the investigation of the effects of nutrient structures on the mixing homogeneity, three distinct categories of nutrient structures were discovered: irregular spheres, irregular rectangles, and irregular plate-like crystals, each exerting unique effects on dry-mixing homogeneity. Although MicroNIR can serve as a technique to determine mixing endpoints, this does not imply that the RSD values of all nutrients are less than 10%. This study not only establishes a method for identifying formula mixing endpoints but also provides a theoretical foundation for real-time monitoring of the mixing process.