The possibility of co-infection with other respiratory pathogens in COVID-19 remains unclear. This study aims to expand the knowledge of distribution and associated factors of co-infection in COVID-19 patients, and to assess the impact of co-infection on COVID-19 prognosis. Both univariate and multivariate analysis were performed to identify independent factors for co-infection. Cox regression was conducted to detect the association between co-infection and negative conversion after controlling other related factors. The rate of co-infection with at least one of other respiratory pathogens was 76.4%. 83.3% of co-infection cases were detected bacterial co-infection, followed by 31.0% with viral co-infection. Over 70% of neutrophils proportion (OR: 4.563; 95%CI: 1.116-18.648) was independently factors for bacterial co-infection, but fever (HR: 4.506; 95%CI: 1.044-19.441) and chest tightness (OR: 0.106; 95%CI: 0.015-0.743) for viral co-infection. The strongest promotion of negative conversion was detected with co-infection of only viruses (HR: 4.039; 95%CI: 1.238-13.177), and the weakest was found for co-infection of only bacteria (HR: 2.909; 95%CI: 1.308-6.472). The promotion of mixed bacteria and viruses was between co-infection of only bacteria and only viruses (OR: 3.242; 95%CI: 1.171-8.977). A higher proportion of bacterial co-infection is detected in comparison with viral co-infection among COVID-19 patients. Over 70% of neutrophils proportion, fever and chest tightness are independent factors associated with specific co-infection in SARS-CoV-2 infection. Additionally, different types of co-infection could variously result in a promoted negative conversion of COVID-19.