Cation ordering in minerals at high temperatures is important for understanding the metamorphic processes in the interior of the Earth. Omphacite, (Na0.5,Ca0.5)(Al0.5,Mg0.5)Si2O6 undergoes an order transition from C2/c to P2/n at about 865 °C. In the transition, the degree of Mg, Al order on two alternate M1 sites is coupled with the Ca, Na ordering on two alternate M2 sites to maintain local charge balance. The determination of diffraction intensities related with cation ordering in omphacite is, therefore, important to understand the kinetics of the cation ordering in omphacite and its thermal history in metamorphic rocks. Here we report the determination of diffraction intensities of an ordered omphacite by using precession electron diffraction (PsED) in a transmission electron microscope (TEM). An ordered omphacite (Jd39Hd4Acm1Di52) from a kyanite-free eclogite in the Münchberg Massif, Bavaria, Germany was investigated. The selected area electron diffraction (SAED) pattern of the omphacite is recorded on a CCD camera using a precession mode in TEM. To evaluate the degree of the cation ordering in omphacite, the intensities of the reflections with h + k = odd, e.g., (050) and h + k = even, (060) were integrated with a gaussian function. The obtained intensity ratio of 0.06(1) in the (050)/(060) reflections from the PsED was comparable with 0.067(5) of the single crystal X-ray diffraction data of the omphacite from the same rock. Using PsED in TEM, we measured pseudo-kinematical diffraction intensities of omphacite, resulted in evaluating the cation ordering state in omphacite at the submicrometer scale.