The effects of concentration and sonication on the liquid crystalline phases of collagen were investigated by several methods, especially by the atomic force microscopy (AFM). The X-ray diffraction (XRD) results revealed that the triple-helical structure of the collagen was nearly unchanged after sonication. Moreover, the differential scanning calorimetry (DSC) examinations indicated that the thermal stability of the sonicated collagen was close to that of native collagen. The AFM observations showed that collagen with a concentration of 60 mg/mL had more ordered arrays compared to that of 30 mg/mL when both samples were treated by sonication. Furthermore, the 60 mg/mL collagen solution without sonication could still form pre-cholesteric patterns, while the liquid phase could not be observed for the 30 mg/mL collagen solution under the same conditions. Generally, AFM was an effective tool for the study of the liquid crystalline phases of collagen.