The invention provides a hexagrammos otakii population dynamic DEB-IBM model and a modeling method. The model comprises two types of model entities including individuals and an environment; the individuals are divided into embryos, juvenile fishes, male adult fishes and female adult fishes according to ages and genders, wherein the life history characteristics of the individuals are represented by four state variables in a hexagrammos otakii DEB model, namely a structure, L, cm, energy reserve, E, J, development, EH, J and breeding cache, ER, J; and according to the environment, the state variables comprise a temperature time sequence and a food concentration time sequence. The modeling method comprises the following steps of (1) defining the state variables and parameters; (2) performing a model initialization process; (3) establishing a running program; (4) adding a sub-model; and (5) running the model. According to the model and the modeling method, energy is used as flux in a model framework and penetrates through the whole life cycle and population changes, so that the problem that the parameters are not easy to obtain is solved to a great extent, and the coupling process of the fish population model and an external environment module is optimized.