This study aims to estimate Ocean Thermal Energy Conversion (OTEC) resources in Indonesian Seas using six years (from 2011 to 2016) daily basis data resulted from numerical simulation of high-resolution (1/10°) ocean model, namely Japan Coastal Ocean Predictability Experiment (JCOPE), with covering a wide area (e.g. 9°N to 11°S and 95°E to 141°E). Estimation of thermal power resources was calculated based on temperature differences between surface layer and deep layer with water depth of 20 m and 1000 m from sea surface respectively. The net output power generated from OTEC and also OTEC operation is sensitive to the fluctuation of the temperature differences, therefore we also analyzed sea surface temperature variability in Indonesia Seas, in order to identify suitable waters area for OTEC operation. We found that Southern coast of Java, Nusa Tenggara and Banda waters are unsuitable for OTEC deployment area because of high temperature variability on the sea surface that can cause instability of power output from OTEC operation. The area, where is favorable for OTEC operation in Indonesia waters, is estimated about 3,773,552.7 square kilometers with total potential power rate that can be harvested around 451.7 GW per day. Surface temperature in Indonesia Seas is also influenced by global phenomena, namely the El Niño and the La Niña. When the El Niño occurs in 2015 to 2016, potential thermal power resources are decrease into 442 GW. Meanwhile, when the La Niña occurs in 2011 to 2012, the OTEC power resources are increase to 460 GW.