Biogas slurry (BS) plays a vital role in improving the efficiency of crop production. On the flip side, the impact of BS on plant lodging factors and yield related traits is still obscure. Hence, we aimed to study the effects of pig and cow BS applications on yield formation, morpho-anatomical, mechanical, physiological properties and transcript expression patterns. The results showed that the yield and lodging resistance of rapeseed were synergistically improved via applying full BS dosage versus nitrogen fertilizer (CK). In addition, the seed yield was significantly increased by 23.9 % by promoting the dry matter accumulation and transport-ability, increasing number of pods by 8.4 % and 1000-seed weight by 5.1 %, respectively. Moreover, BS developed the stem mechanical strength by decreasing lodging index by 34.2 %, which was manifested by an increase in stem thickness and stiffness and a reduction in plant height. Besides, it enhanced the photosynthesis through promoting chlorophyll synthesis, delaying plant senescence, and accumulating N and K concentration. Anatomical observations revealed that BS increased greater number and area of stem vascular bundles, vessels, and maintained a dense microstructure than CK. Also, it boosted pectin, Ca2+ and K+ contents, which were significantly positively correlated with stem mechanical strength and reduced cellulose, lignin and hemicellulose contents. Meanwhile, correlation and structural equation modeling analysis validated the above results. Additionally, the differentially expressed genes were enriched in cell wall formation pathway, especially about the biosynthesis of pectin (PME, PG and PL), cellulose (CesA and CSL), lignin (PAL, POD, CCR, LAC and COMT) and hemicellulose (XTH and Xyl) were identified under BS. The above-mentioned results indicated that BS simultaneously affected lodging behavior by altering structural carbohydrates and modified yield composition by regulating dry-matter accumulation and allocation. This is the first comprehensive strategy on synchronizing rapeseed yield increase and lodging resistance under optimized BS management.