The increasing popularity of the online manuscript submission system has brought great convenience for authors to submit manuscripts and expert reviewers, and improved the efficiency of editing and publishing work and the transparency of manuscript processing. However, it also provides convenience for the occurrence of academic misconduct such as "multiple submissions". Academia and publishing workers pay more attention to and research on "multiple submissions", but the phenomenon has not attracted the attention of researchers, and there is little attention and research in academic circles. In fact, the phenomenon is becoming more and more serious. This paper takes three academic journals as research cases, and discusses the submission characteristics of "multiple submissions" papers in the online manuscript submission system of academic journals, to enhance the screening and prevention of "multiple submissions", and to attract the attention of academic journals and editors to "multiple submissions" papers and reduce the negative impact of such papers on journal editing and publishing. Through the query and statistics of all submissions in thethree journals’ online submission system from January to December 2020, a total of 2664 "multiple submissions" papers are obtained. This paper summarizes the characteristics of "multiple submissions" papers according to the author’s e-mail username format, the same author registering multiple usernames, etc. This paper discusses the occurrence logic of "multiple submissions" papers from the perspectives of the bad orientation of "thesis-only" in talent evaluation, the development of network technology and the imperfection of submission system, and the authors’ own utilitarian scientific research mentality. This paper analyzes the negative impacts of "multiple submissions" from the perspectives of creating a "bubble" of manuscript sources, wasting journal publishing resources, risking "multiple submissions" or even "multiple publications", being not conducive to the acceptance of manuscripts, and delaying the author’s publication progress. In order to reduce the adverse effects and harm of "multiple submissions", corresponding governance measures are proposed from the perspective of multi-subject collaborative governance. Universities and scientific research institutions should get rid of the bad orientation of "thesis-only" and establish a more scientific and reasonable talent evaluation system. Authors should raise their awareness, recognize the adverse effects of "multiple submissions", and take the initiative to eliminate "multiple submissions". Editors should be more vigilant, give full play to their subjective initiative, and effectively identify "multiple submissions". Journals should strengthen system maintenance and website management, and prevent "multiple submissions" from technical upgrades and management systems. Government departments should increase punishment of intermediary agents for papers, and purify the atmosphere of academic research. Only when all relevant subjects improve their ideological understanding, take the initiative to act, and take multiple measures to form a system synergy and improve governance efficiency, can they effectively prevent and even completely eliminate "multiple submissions", create a good academic ecology, and better promote academic journals healthy and sustainable development.