The objective of this study was to determine the effect of whole flaxseed and ground flaxseed supplementation on the composition of fatty acids in plasma and milk, particularly the content of omega-3 polyunsaturated fatty acids (n-3 PUFAs). Thirty Holstein dairy cows were randomly assigned to three treatment groups. Cows were fed a total mixed ration without flaxseed (CK), 1500 g of whole flaxseed (WF), and 1500 g of ground flaxseed (GF) supplementation. There were no differences observed in dry matter intake, milk yield, energy-corrected milk, and 4% fat-corrected milk (p > 0.05). Compared with the CK group, the contents of α-linolenic acid (ALA), eicosatrienoic acid, and eicosapentaenoic acid increased in the plasma and milk WF and GF groups, and the content of docosahexaenoic acid and total n-3 PUFA was higher in GF than the other groups (p < 0.001). The ALA yield increased to 232% and 360% in WF and GF, respectively, compared to the CK group. Compared with the WF group, GF supplementation resulted in an increased milk ALA/ALA intake ratio (p < 0.001). Flaxseed supplementation increased the activity of GSH-Px and decreased the concentration of MDA in milk (p < 0.001). Plasma parameters did not differ among the treatments (p > 0.05). This result indicated that compared with the WF group, GF supplementation in the diet showed higher efficiency in increasing the total n-3 PUFA levels and the milk ALA/ALA intake ratio, and decreased the ratio of n-6 PUFAs to n-3 PUFAs in milk.