Outdoor air pollution and indoor burning of biomass fuel can cause high blood pressure. However, little is known about the effects of cooking with clean energy on hypertension. We thus explored whether cooking with clean energy is associated with the risk for hypertension. The study used baseline data from 12,349 women from a large population-based cohort study in Beijing, China. Information on cooking habits, health status, and other characteristics was collected by questionnaire and physical examination. Fasting blood samples were collected to measure total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and homocysteine (HCY). An index of cooking exposure was constructed. Logbinomial regression models were used to estimate the association between cooking exposure and risk for hypertension. The prevalence of hypertension was 26.7%. Any cooking exposure at all was associated with an increased risk for hypertension with an adjusted prevalence ratio (aPR) of 2.27 (95% confidence interval [CI]: 2.01, 2.57). The risk for hypertension increased with increases in cooking frequency, time spent cooking, and the cooking index, all showing a dose-effect relationship (P < 0.001). An increased risk for hypertension was associated with both cooking using mainly electricity (aPR: 1.75, 95% CI: 1.41, 2.17) and cooking using mainly natural gas (aPR: 2.30, 95% CI: 2.03, 2.60). The cooking index was positively correlated with plasma concentrations of TC, TG, LDL-C, and HCY and negatively correlated with HDL-C. Abnormal levels of all these biomarkers were associated with an increased prevalence of hypertension after adjustment for confounding factors.