An eddy-resolving four-dimensional variational (adjoint) data assimilation and state estimate was constructed for the low- to mid-latitude Pacific, Indian Oceans, and South China Sea based on the framework of “Estimating the Circulation and Climate of the Oceans (ECCO)”. It is named as the Two Oceans One Sea State Estimate (TOOSSE). It fits a model to a number of modern observations of 2015–2016, including the Argo float temperature and salinity, satellite altimetric sea surface anomalies, by adjusting initial temperature and salinity, sea surface boundary conditions, and background diapycnal diffusivities. In total, ～50％ of the original model-data misfits have been eliminated, and the estimated state agreed well with a variety of independent observations at meso- to large scales, and on the intra-seasonal to interannual timescales. Mesoscale variability is systematically strengthened in TOOSSE and closer to observations than that without data assimilation, which is especially evidenced by the improved simulation of the mesoscale tropical instability waves (TIWs). Adjustments to ocean surface forcing parameters exhibit both large and frontal/mesoscale structures, and the magnitude reach 20％–100％ of the first guesses; the adjustments to diapycnal diffusivity exhibit an obvious elevation (decrement) in (below) the thermocline in the equatorial band. The results indicate that TOOSSE represents a dynamically and thermodynamically consistent ocean state estimate of the 2015–2016 Indo-Pacific Ocean, and can be widely utilized for regional process studies.