Healthy diets are necessary for both humans and animals, including poultry. These diets contain various nutrients for maintenance and production in laying hens. Therefore, research was undertaken to explore the efficiency of various dietary flaxseed sources on the n-3 deposition in the egg yolk and gene expression in laying hens. Five dietary groups were analyzed, i.e., (i) a corn-based diet with no flaxseed (FS) as a negative control (NC), (ii) a wheat-based diet supplemented with 10% whole FS without multi-carbohydrase enzymes (MCE) as a positive control (PC), (iii) ground FS supplemented with MCE (FS), (iv) extruded flaxseed meal was supplemented with MCE (EFM), (v) flaxseed oil supplemented with MCE (FSO). Results indicated that egg weight was highest in the NC, FS, EFM, and FSO groups as compared to PC in the 12th week. Egg mass was higher in enzyme supplemented groups as compared to the PC group, but lower than NC. In the 12th week, the HDEP (hen day egg production) was highest in the FS and EFM groups as compared to FSO, PC, and NC. The FCR (feed conversion ratio) was better in enzyme supplemented groups as compared to the PC group. Enzyme addition enhanced the egg quality as compared to PC in the 12th week. The HDL-C (high-density lipoprotein cholesterol) was increased, while LDL-C (low-density lipoprotein cholesterol), VLDL-C (very-low-density lipoprotein cholesterol), TC (total cholesterol), and TG (total triglycerides) were reduced in the enzyme supplemented groups as compared to PC and NC. The FSO deposit more n-3 PUFA and docosahexaenoic acid (DHA) in the egg yolk as compared to FS and EFM groups. The expression of ACOX1, LCPT1, FADS1, FADS2, and ELOV2 genes were upregulated, while PPAR-α was downregulated in the FSO group. The LPL mRNA expression was upregulated in the FS, EFM, and FSO groups as compared to the PC and NC groups. It was inferred that FSO with enzymes at 2.5% is cost-effective, improves the hen performances, upregulated the fatty acid metabolism and β-oxidation genes expression, and efficiently deposits optimal n-3 PUFA in the egg as per consumer’s demand.