[Purposes] The current situation of two-dimensional codes integrated into a single paper is investigated and analyzed to provide basis for promoting and standardizing the application of two-dimensional codes in scientific papers. [Methods] Taking the member journals in the website of Society of China University Journals as samples, we investigated the number of journals with two-dimensional codes integrated into single papers, as well as their location, size, style, quotation, and link content. [Findings] Among 213 scientific journals sponsored by Chinese universities, 24.9% of them integrate two-dimensional codes, and their positions are widely distributed, with large size differences. Among 53 journals with two-dimensional codes, 60.4% of them have no code quotation. In addition, the validity and value of the link content are not paid enough attention to. Among 22 journals linked with OSID, only 2 journals have author audio in all codes, other journals have audio in some codes, and only 5 of 460 codes have video. [Conclusions] The form and content of two-dimensional code in a single paper of scientific journals have a great change space. Its normative application in scientific journals needs to be promoted through the publishing departments, authors, and the journal management departments.