Target detection is very difficult with complex clutters in IRST(Infrared Search and Track) system for a long distance target. Especially sea-clutter and ocean-surface with non-uniform temperature distribution make it difficult to detect incoming targets in images obtained in sea environment. In this paper, we propose a novel method based on morphological method for estimation of ocean surface with non-uniform temperature flow. In order to estimate the exact ocean surface temperature flow, we divided it into upper and lower bound flow. And after estimating it, the final ocean surface temperature flow is derived by a mean value of the estimated results. Also, we apply the multi-weighted technique with a variety of sizes of structure elements to overcome sub-sampling effect by using morphology method. Experimental results for ocean surface images acquired from many different environments are compared with results of existing method to verify the performance of the proposed methods.