The Complex Empirical Orthogonal Function (CEOF) analysis is applied to discuss the modes and results of abnormal upper circulation over the tropical Indian Ocean in winter. The main conclusions are as follows. The first and second leading modes of the current anomalies are trapped by the equator wave, which decay rapidly poleward from the equator and show a zonal flow pattern. The natures of the first and second modes are the half wave pattern and full wave pattern of the equatorial ocean wave, respectively. This indicates that the equatorial wave anomaly plays an important role in the oceanic flow anomaly. The near-surface sea temperature anomaly resulted from the abnormal vertical motion of the first mode in the winter is different from that in the spring and autumn. In this situation, the distribution of meridional sea temperature anomaly near the equatorial Indian Ocean presents a "+-+" pattern. It is different from Indian Ocean Dipole (IOD) and is the direct reason for the declining of IOD in winter. The sea temperature anomaly corresponding to the second mode presents a pattern of north-negative and south-positive. The first mode is closely related to South Asian winter monsoon anomaly. Both modes demonstrate significant inter-annual and inter-decadal variations. The period of their inter-annual variation is about 3-5 years. The main periods of their inter-decadal variations are about 18 and 22 years, respectively, while they also have a period of about 13 years. The main inter-decadal variations of the first and second modes discussed in this paper correspond to the main inter-decadal variations of the second and first modes of circulation anomaly over the North Pacific and tropical Pacific in winter.