The conceptual framework defines ecological risk as the characterization of the adverse ecological effects of environmental exposures to hazards imposed by natural changes or human activities. Ecological risk assessment is a flexible process for organizing and analyzing data, assumptions, and uncertainties to evaluate the likelihood (probability) of adverse ecological effects that may have occurred or may occur as a result of exposure to one or more stressors related to sources of ecological risk. It can provide a reliable quantitative evidence for the ecological environment risk management and decision-making. The ecological risk assessment can be divided into three regimes according to the classification standard for the characters of the risk source, including risk assessment of chemical pollution risk source, ecological assessment of ecological events risk source and risk assessment of composite risk source (natural risk source and human activities risk source). This paper reviews the recent developments surrounding concept of ecological risk and discusses the future research directions of three methods of ecological risk assessment. The improved quotient method is more quantificational than the old one by setting multiple levels of risk or giving the value of risk, and the further study of this method may be focused on reflecting the relationship between the concentration of pollutants and the effects of the contaminated receptors, estimating influence of pollutants on receptors which are not in the study sites and calculating the range of being polluted or damaged. When the acute toxicological effects is analyze by the exposure-response method to assess ecological risk in the controlled conditions, it is important to analyze the secondary effects of pollutants on objective environment and changes of receptors effects caused by transformation as well. The research of the invasive risk assessment of non-indigenous species is still in the stage of constructing the regime and has not yet formed a same conclusion. This paper argues that we can establish a unified index system through decomposing the indicators of layer guidelines by defining the connotation, extension and the numbers of the specific indicators which corresponding to each layer group, and the “threshold value” of the indexes should be investigate accurately which reflect the capacity of the environment. Furthermore, we suggest that statistical method could be used as an assistant way to prompt the accuracy of the assessment when the ecological niche model is used to evaluate the invasive risk of non-indigenous species. The three-tiered of the procedure for ecological tiered assessment of risks (PETAR) is adapted to evaluate the ecological risks in the case of limited resources or scarce background information of relevance. The priority of the study of the ecological risk assessment should be given three aspects to prompt the availability of the assessment results for the ecological risk management, one is a systematic database of the acute and chronic toxicity data, the other is a unified evaluation regime or national standards to evaluate the invasive risk of non-indigenous species, and the way which using statistical method, complex systems theory and remote sensing technology to assess the ecological risk.