The paper aims to seek a reasonable ratio of organic and chemical fertilizers application for cigar tobacco production, so as to improve the quality of cigar tobacco. This study was carried out in Suijiang County, Zhaotong City, Yunnan Province. Using ‘Yunxue No.39’ as the material, the effects of replacing chemical fertilizers with organic fertilizers proportionally on the appearance quality, agronomic traits, yield and quality and chemical intrinsic quality of cigar tobacco leaves were studied. The results indicated that the replacement of chemical fertilizers with organic fertilizers can effectively enhance the color, oil content, and quality of modulated cigar tobacco leaves; the height of the cigar tobacco plants, stem circumference, leaf area, and leaf area coefficient initially increased with the amount of organic fertilizer substitution, followed by a subsequent decline. Notably, substituting 40% of the chemical fertilizer with organic fertilizer significantly improved the agronomic traits; the yield and output value of cigar tobacco leaves increased with the reduction of inorganic fertilizers; compared with the conventional application of fertilizers, utilizing organic fertilizers to replace chemical fertilizers by 20%, 40% and 60% resulted in yield increases of 1.83%, 8.2% and 4.57%, respectively. Correspondingly, the output value increased by 5.09%, 13.6% and 7.45%, respectively, significantly increasing the economic benefits; with the increase of proportion of organic fertilizer replacing chemical fertilizer, the total sugar, total nitrogen, water-soluble chlorine, potassium oxide, K/Cl ratio, reducing sugar to total vegetative base ratio, and total nitrogen to total plant base ratio of cigar tobacco progressively aligned with those of high-quality domestic and foreign cigar filler leaves. Notably, the most significant improvements were observed when 40% of the chemical fertilizer was substituted with organic fertilizer. This practice not only enhances the quality of tobacco leaves but also boosts the economic benefits associated with tobacco cultivation. In summary, using organic fertilizer to replace 40% chemical fertilizer in cigar tobacco cultivation can effectively improve the quality and increase the economic benefits of tobacco.