In juridical practices, ecological environment standards are included in the “national regulations” in Articles 1234 and 1235 of the Civil Code and are used for the trial of ecological and environmental damage cases. Both national and local ecological environment standards are applicable, mainly including pollutant emission standards and ecological environment quality standards. Moreover, only those who cause ecological and environmental damage while violating ecological environment standards will be convicted of violating “national regulations”. Ecological environment standards have multiple impacts on fact determination and legal application. In order to further understand this phenomenon, Luhmann’s System Communication Theory was used as the analytical framework. Based on the empirical study of 71 cases of ecological and environmental damage, the interactive process between systems caused by ecological environment standards was explained, giving play to the “observation for observation” advantage of the legal system over other social sub-systems. At present, the inclusion of ecological environment standards in the Civil Code has such problems as insufficient or excessive compensation for ecological and environmental damage due to the contradictions and gaps in the application of ecological environment standards, the lack of comprehensive consideration of environmental public interests and other public interests, the excessive dependence on the virtual governance cost to calculate the amount of compensation for ecological and environmental damage. The following suggestions are proposed for these problems. Firstly, the boundary and division standards for the ecological environment standards to be included in “national regulations” should be clearly defined, so as to ensure the unification and operability of standards. Secondly, the organic integration of “fact” and value should be promoted in the judicial application of ecological environment standards by perfecting procedures and entity rules, in order to balance the conflicts among multiple values. Thirdly, the methods and procedures for the identification, evaluation and judicial application of ecological and environmental damage should be improved. In the meanwhile, high-quality ecological environment standards and judicial interpretations should be timely updated.