Flaxseed and walnuts are rich sources of polyunsaturated fatty acids (PUFA), but the effects of these foods on metabolic syndrome have not been investigated. For that purpose, a randomized controlled trial was conducted among 283 Chinese participants to compare three interventions of lifestyle counselling with supplementation of either flaxseed (30 g/day) or walnuts (30 g/day) and a control group. The study sample included 239 patients with clinically confirmed metabolic syndrome and 44 with two components of metabolic syndrome. All participants were instructed to follow a general healthy lifestyle according to AHA guidelines. After the 12-week intervention, a 16.7% reduction in the prevalence of the metabolic syndrome was observed. Participants who added flaxseed or walnuts to their diet did not gain weight and even showed slight additional benefits on central adiposity compared with the control group. Moreover, among participants with central obesity at baseline, flaxseed incorporation seemed to decrease fasting glucose and prevent the increase of HbA1c. These results indicate a favourable impact of a lifestyle counselling intervention for the management of Chinese individuals with the metabolic syndrome as well as the additional benefits of flaxseed and walnut supplementation on central obesity and glycemic control. Further studies are needed to understand the role of these foods on the metabolic syndrome.