Starting with the role of system analysis in lake ecosystem research, this paper summarized the tentative procedures and softwares for studying the dynamics of lake ecosystem. There are several main stages in modeling the dynamics of lake ecosystem, namely, problems identification, mathematical formulation, computation, validation, sensitive analysis, calibration, and verification. In the modeling, selecting temporal and spatial scales is essential but complex. Since 1960s, a rapid progress has been made in modeling the dynamics of lake ecosystem, being developed from simple zero-dimension models to complex ecological-aquatic-hydrodynamic ones, among which, exergy was applied popularly as an objective function in modeling. In this paper, LakeWeb and LEEDS (Lake Eutrophication, Effect, Dose, and Sensitivity model) were analyzed as examples. In China, the development of lake ecosystem dynamic models could be traced back to 1980s, and most of them were focused on Lake Dianch, Lake Taihu, Lake Chaohu and Lake Donghu. Some softwares such as CE-QUAL-ICM, WASP, AQUATOX, PAMOLARE and CAEDYM were developed to simulate lake ecosystem dynamics, among which, CE-QUAL-ICM is more suitable for long and narrow water bodies. WASP consists of three parts, i. e., DYNHYD, EUTRO, and TOXI. AQUATOX is an ecological risk model, and the parameters are mainly calibrated in U. S. A, which has limited its further application in China. The software ECOPATH for simulating the energy flows in lakes was also described in this paper. There are still many shortages in the lake ecosystem dynamic models, e. g., the lack of sufficient monitoring data for validation, insufficient consideration of uncertainties and the role of bacteria, and inconsistent relationship with watershed changes. The uncertainties are mainly from the intrinsic uncertainties in aquatic ecosystem, in modeling, in parameters selection, and also in forecast and application. Setting up long-term monitoring and data sharing mechanism, using interpolation to make data more densely, introducing objective functions, dealing with uncertainties, and constructing watershed-lake ecosystem dynamic model could be the available ways for overcoming the shortages.