Preprint scholarly communication system construction, with preprints as the carrier and preprint platform as the medium, can effectively accelerate the transformation of innovative research results and provide intellectual support and power guarantee for scientific and technological innovation. This study applies the ecosystem theory to elucidate the composition and interaction mechanism of the multi-level system of preprint scholarly communication system, analyses the existing problems, and proposes corresponding strategies based on pieces of evidence, including the literature research results, the network research data of mainstream preprint platforms, and the relevant events and case analyses. It found that uncertain attitudes of researchers towards preprints, the lack of cooperation between preprint platforms and journal publishers, and the separation of preprints in the mainstream academic system have hindered the interactive symbiosis of micro-, meso- and macro-ecosystems in the preprint scholarly communication system. Therefore, it is necessary to enhance the researchers’ recognition of preprints, strengthen the synergies between preprint platforms and journal publishers, and promote the integration of preprints into the mainstream academic system.