Although previous studies showed that biochar can mitigate methane emissions through microbial activities from paddy fields, little is known about its effects on salt-affected soil. The current study aims to examine the interactive effect of biochar and cow manure (CM) on (1) methane emissions from salt-affected soil and (2) methanogenic and methanotrophic activities to identify potential mechanisms for the emissions. A two-factor pot experiment was set up, following a randomized complete block design with four replicates. Paddy rice (Oryza sativa L.) was grown on six treatments (no CM + no biochar; no CM + rice husk biochar; no CM + rice straw biochar; CM + no biochar; CM + rice husk biochar; CM + rice straw biochar). Methane emissions from salt affected soil were relatively low and CM addition significantly increased CH4 emissions (by 801%). For the CM treatments, biochar addition significantly reduced methane emissions (by 28 to 680%), but for the non-CM treatments, biochar addition showed no clear effect. The increase in methane emissions by CM could be involved in the improved relative abundance of methanogenic and methanotrophic genes. In contrast, the reduction of methane emissions by biochar was likely related to the reduced abundance of methanogenic and increased that of methanotrophic genes. In brief, low methane emissions from salt-affected soil were increased by CM addition and biochar addition could mitigate the CM's effect. Balancing methanogenic and methanotrophic activities could serve as a major mechanism in determining methane emissions from salt-affected soil added with cow manure and biochar.