In order to study the effect of high-yield 3-methylbutyraldehyde Lactococcus lactis YN2-1 on the flavor of cheddar cheese, it was added to cheddar cheese as an auxiliary starter culture. The aroma characteristics and volatile compounds of different cheddar cheese samples were compared and analyzed by sensory quantitative description analysis, gas chromatography-mass spectrometry (GC-MS), gas chromatography-ion mobility spectrometry (GC-IMS) and electronic nose. Firstly, in the quantitative descriptive analysis and preference evaluation of the samples, it was found that the cheddar cheese added with Lactococcus lactis YN2-1 had significant aroma differences with the samples without the addition of the bacteria. The cheese added with YN2-1 had higher nut flavor, milk flavor and broth flavor aroma intensity, and its preference score was also higher. GC-MS analysis showed that the content of 3-methylbutyraldehyde in cheese samples added with Lactococcus lactis YN2-1 and matured for 60 d and 120 d was 18.43 μg/kg and 13.96 μg/kg, respectively, which was significantly higher than that of the control group, indicating that the strain has the characteristics of high yield of 3-methylbutyraldehyde in cheddar cheese. The GC-IMS fingerprint was used to visually distinguish the differences in flavor substances between the cheddar cheese added with Lactococcus lactis YN2-1 and the control sample. The contents of 2,3-butanedione, 2-pentanone D, 2-nonanone, 2-methylbutanal, n-propanol, butyl acetate, butyl butyrate, 2,5-dimethylpyrazine, 2-ethyl-3,5-dimethylpyrazine and other substances increased significantly in 60 d or 120 d samples. The contour of the electronic nose radar map between different samples did not overlap, and the discrimination factor (DFA) was higher, indicating that there was a significant difference between the cheese samples added with YN2-1 strain and the control samples, which verified the analysis results of GC-MS and GC-IMS. Conclusion: The addition of this strain could not only increase the content of 3-methylbutyraldehyde, but also contribute to the increase of other flavor substances in cheese. It had a significant improvement effect on the nutty, milky and fruity aroma of cheddar cheese, and has good application potential.