Impacts of the Indonesian Throughflow (ITF) on seasonal circulation in the equatorial eastern Indian Ocean are investigated using the ocean-only model LICOM by opening and closing ITF passages. LICOM had daily forcing from NCEP reanalysis data during 2000–2011. It can reproduce vertical profiles of mean density and buoyancy frequency of World Ocean Atlas 2013 data. The model also simulates well annual oscillation in the central Indian Ocean and semiannual oscillation in the eastern Indian Ocean of sea level anomalies (SLA) using satellite altimeter data, as well as the semiannual oscillation of surface zonal equatorial currents of Ocean Surface Current Analyses Real Time current data in the equatorial Indian Ocean. The wave decomposition method is used to analyze the propagation and reflection of equatorial long waves based on LICOM output. Wave analysis suggests that ITF blockage mainly influences waves generated from the Indian Ocean but not the Pacific Ocean, and eastern boundary reflections play an important role in semiannual oscillations of SLA and zonal current differences in the equatorial Indian Ocean associated with ITF. Reconstructed ITF-caused SLA using wave decomposition coefficient differences between closed and open ITF-passage experiments suggest both Kelvin and Rossby waves from the first baroclinic mode have comparable contributions to the semiannual oscillations of SLA difference. However, reconstructed ITF-caused surface zonal currents at the equator suggest that the first meridional-mode Rossby wave has much greater contribution than the first baroclinic mode Kelvin wave. Both reconstructed sea level and zonal currents demonstrate that the first baroclinic mode has a greater contribution than other baroclinic modes.