Species safety risks brought by the development of modern biotechnology have become an essential topic for urgent consideration in national biosecurity. Species diversity risk, species quality risk, species habitat risk, and risk from alien species invasion are crucial representations of species safety risks of modern biotechnology. The limited scientific cognition ability, the negative values caused by technological alienation, and the limitation of STI risk governance ability are the important causes of species safety risks. In order to strengthen species safety risk management and promote the healthy development of modern biotechnology, the “government-science community-civil society” should form a flexible governance model with equal interaction and democratic consultation among multiple actors. Specifically, the government should clarify the leading position of governance, improve the national species safety strategy, relevant laws and institutional systems and inter-ministerial coordination mechanism to enhance the risk governance capacity; the scientific community should actively assume social responsibility, promote the Scientific Spirit, adhere to Responsible Innovation and improve the institutionalized consultation and dialogue mechanism to enhance the voice; civil society should actively participate in STI governance process through strengthening the support of non-governmental organizations, effectively playing the role of the media, and safeguarding and exercising public rights in order to exert the role of monitoring and feedback.