This study investigated the changes in the characteristics of goat milk protein in the presence of trehalose, chitooligosaccharide and pectin during two practical dairy processing operations of pasteurisation and spray drying. The highest denaturation temperature and the largest particle size of milk protein were found in goat milk added with pectin after pasteurisation. And particles with more uniform and compact morphology were observed in goat milk protein with these three saccharides. An elevated emulsifying activity index of 24.37 m/g−2 was observed in protein after spray drying due to chitooligosaccharide. And the foam stability was also improved significantly in the presence of trehalose and pectin during pasteurisation. During spray drying, saccharides showed the stabilizing effect on goat milk protein. This study revealed a complex interplay between the type of saccharides and the processing operation applied to goat milk, which might be of great significance for the production and processing of goat milk.