Citizen science refers to the participation of people with scientists, researchers, and policy makers to provide solutions for problems in society, and its successful implementation requires public cooperation in the public issues. The participation of a large group of people with different backgrounds and interests may result in moral problems. The purpose of this study is to identify the ethical challenges in the participatory approach of citizen science with respect to different Performers, actors and stakeholders, and to provide solutions for them. In this regard, first, reviewing the existing literature on ethics in citizen science and crowdsourcing, ethical issues that should be considered have been identified. Then, employing Soft Systems Methodology, the problem was structured, and accordingly, some implications based on the conditions and situation of the problem were proposed. The statistical population of the study was eleven expert including four academic experts with a background in the field of participatory projects and four experts with executive experience, as well as three lawyers. The findings of this study were based on the interpretation of interviews with experts. According to the results, in order to overcome the challenges, there is a need for changes in the ethical system of citizen science participatory projects. These changes include, scrutinizing the enacting process and implementation of laws, strengthening the infrastructure, direct and continuous monitoring of the implementation process, providing participation conditions for all volunteers, compensation of services in accordance with efforts and skills of participants, training of volunteers, process transparency and interact with participants, set standards, and share authorized information with the community at the appropriate time.