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Based on widely used remote sensing ocean net primary production (NPP) datasets, the spatiotemporal variability of NPP is first analyzed over the tropical eastern Indian and western Pacific Ocean for the period 1998-2016 using the conventional empirical orthogonal function (EOF), the lead-lag correlation and the ensemble empirical mode decomposition (EEMD) technique. Barnett and Preisendorfer's improved Canonical Correlation Analysis (BPCCA) is also applied to derive covariability patterns of NPP with major forcing factors of the chlorophyll a concentration (Chla), sea surface temperature (SST), sea level anomaly (SLA), ocean rainfall (Rain), sea surface wind (Wind), and current (CUR) under climate changes of El Nino-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD). We find that: (1) The first two seasonal EOF modes capture significant temporal and meridional NPP variability differences, as NPP reaches peaks approximately three months later in the western Pacific Ocean than that of in the eastern Indian Ocean. (2) The second and third interannual EOF modes are closely related with ENSO with a two-month lag and synchronous with IOD, respectively, characterized by southwesterly positive anomaly centers during positive IOD years. (3) NPP presents different varying tendencies and similar multiscale oscillation patterns with interannual and interdecadal cycles of 2 3 years, 5 8 years, and 9 19 years in subregions of the Bay of Bengal, the South China Sea, the southeastern Indian Ocean, and the northwestern Pacific Ocean. (4) The NPP variability is strongly coupled with negative SST, SLA, and Rain anomalies, as well as positive Chla, Wind and CUR anomalies in general during El Nino/positive IOD years. The results reveal the diversity and complexity of large-scale biophysical interactions in the key Indo-Pacific Warm Pool region, which improves our understanding of ocean productivity, ecosystems, and carbon budgets.