In order to investigate ordered phases revealed at low temperatures in clathrate compound Pr3Pd20Si6, we have performed ultrasonic measurements using a single crystal in magnetic fields at low temperatures. Temperature dependence of elastic constant C-11 and C-L[1 (1) over bar0] = (C-11 + C-12 + C-2(44))/2 shows the anomalies at about 150 mK in zero field. Magnetic phase diagrams are determined by measuring C-11 in H parallel to [001] and C-L[1 (1) over bar0] in H parallel to [111]. The magnetic phase diagrams along the three principal axes indicate a closed loop and a strong magnetic anisotropy. This result suggests that antiferroquadrupole ordering appears at low temperatures in Pr3Pd20Si6.