Flaxseed contains huge quantities of anti-nutritional factors (ANFs), which reduce the performance of livestock. Three different protease and multi-carbohydrase enzymes were included in wheat-flaxseed diets (WFD) and corn-flaxseed diets (CFD) to compare their effects on performance, egg n-3 deposition, and fatty acid transporter genes in laying hens. A total of 540, twenty-week-old, Nongda-3 laying hens (DW brown × Hy-line white) were randomly assigned to six dietary groups, including 10% WFD or 10% CFD plus (i) supplemental enzyme A (alkaline protease 40,000 and neutral protease 10,000 (U/g)), (ii) enzyme B (alkaline protease 40,000, neutral protease 10,000, and cellulase 4000 (U/g)), or iii) enzyme C (neutral protease 10,000, xylanase 35,000, β-mannanase 1500, β-glucanase 2000, cellulose 500, amylase 100, and pectinase 10,000 (U/g)). An interaction (p < 0.05) was found for egg mass, hen day of egg production, and feed conversion ratio on the 9–10th week of the experiment. The WFD with enzyme B was associated with the highest egg weight in the 9–10th week. The deposition of total n-3 was superior with WFD (468.22 mg/egg) compared to CFD (397.90 mg/egg), while addition of enzyme C (464.90 mg/egg) resulted in the deposition of more total n-3 compared to enzymes A and B (411.89 and 422.42 mg/egg). The WFD and enzyme C significantly (p < 0.001) enhanced docosahexaenoic acid (DHA) and reduced the n-6:n-3 ratio in egg yolk compared to the CFD. The hepatic mRNA expression of liver fatty acid binding protein (L-FABP) (p = 0.006), fatty acid desaturase 1 (FADS-1) (p < 0.001), elongase-2 (ELOV-2) (p < 0.001), fatty acid transport protein-1 (FATP1) (p < 0.001), and the intestinal mRNA expression of FATP and FABP genes were increased with WFD compared to CFD. In conclusion, WFD with enzyme C is favorable for optimal performance, results in the deposition of more n-3 and DHA, and increases the expression of fatty acid transporter genes, which helps in n-3 transport.