ZrO2–mullite nanocomposites were fabricated by in-situ-controlled crystallization of Si–Al–Zr–O amorphous bulk at 800–1250°C. The structural evolution of the Si–Al–Zr–O amorphous, annealed at different temperatures, was studied by X-ray diffraction, infrared, Laser Raman spectroscopy, field emission scanning electron microscopy, and high-resolution transmission electron microscopy. The materials consisted of an amorphous phase up to 920°C at which phase separation of Si-rich and Al, Zr-rich clusters occurred. The crystalline phases of t-ZrO2 and mullite were observed at 950°C and 1000°C, respectively. Mullite with a tetragonal structure, formed by the reaction between Al–Si spinel and amorphous silica at low temperature, changed into an orthorhombic structure with the increase of temperature. It was the phase segregation that improved crystallization of the Si–Al–Zr–O amorphous bulk. The anisotropic growth of mullite was observed and the phase transformation from t-ZrO2 to m-ZrO2 occurred when the temperature was higher than 1100°C.