Background: To investigate the influence of hyperhomocysteinemia (HHcy) and metabolic syndrome (MetS) on left ventricular hypertrophy (LVH) in residents in rural Northeast China. Methods: We performed a cross-sectional baseline data analysis of 6837 subjects (mean age: 54 ± 10 years) recruited from a rural area of China. Anthropometric indicators were measured according to standard methods. MetS was defined by the modified ATP III criteria. HHcy was defined according to the WHO standard: an Hcy level > 15 μmol/L representing HHcy. Four groups were defined: non-HHcy & non-MetS, HHcy & non-MetS, MetS & non-HHcy and HHcy & MetS. Results: The left ventricular mass index for height 2.7 (LVMH 2.7) in both sexes was significantly higher in the HHcy & MetS group than in the non-HHcy & non-MetS group (females: 51.23 ± 16.34 vs. 40.09 ± 10.55 g-2.7 , P < 0.001; males: 48.67 ± 12.24 g-2.7 vs. 42.42 ± 11.38 g-2.7 , P < 0.001). A similar result was observed in those groups when using the left ventricular mass index (LVMI) for body surface area to define LVH (females: 103.58 ± 31.92 g − 2 vs. 86.63 ± 20.47 g − 2 , P < 0.001; males: 106.10 ± 24.69 g − 2 vs. 98.16 ± 23.29 g − 2 , P < 0.001). The results of multiple regression analysis indicated that the HHcy & MetS group had a higher risk of LVH than the other three groups (OR: 1.628 for LVMI, P < 0.001, OR: 2.433 for LVMH 2.7 , P < 0.001). Moreover, subjects in the HHcy & non-MetS group [OR (95% CI): 1.297 (1.058, 1.591) for LVMI, P < 0.05; OR (95% CI): 1.248 (1.044, 1.492) for LVMH 2.7 , P < 0.05] also had a statistically greater risk of LVH than subjects in the non-HHcy & non-MetS group. The HHcy & non-MetS group was also found to be significantly and independently associated with LVH. Conclusion: Hyperhomocysteinemia has an independent effect on LVH. The combined effect of MetS and hyperhomocysteinemia might increase the strength of the abovementioned effects.