Jerusalem artichoke (Helianthus tuberosus L.) is an important source of biomass for biofuels production. To evaluate its potential as a feedstock for biofuel, calorific value, ash, and carbon (C) and nitrogen (N) contents were investigated under different flower removal treatments during 2015–2016 in the Inner Mongolia autonomous region of China. Total biomass of flower removal treatments was significantly (P < 0.05) higher than that of the control, and the highest value was obtained when 50 % of the flowers were removed (735 g plant⁻¹). Tuber biomass increasing gradually as the proportion of flowers removed increased. The highest value of tuber biomass was obtained when 100 % flowers were removed (228 g plant⁻¹). Tuber yield of the 33 % and 50 % flower removal treatments was significantly higher than that of the 25 % flower removal treatment and control. The caloric value and N and C contents of tuber was improved while ash content of tuber was decreased with flower removal, compared to no flower removed. Total energy was the highest with removal of 50 % of the flowers 19,041 J plant⁻¹). In contrast, the highest value of aboveground energy yield occurred with removal of 25 % of the flowers (7076 J plant⁻¹), while underground energy yield was greatest with removal of 100 % of the flowers (4058 J plant⁻¹). Removing 100 % flowers is an effective method to increase tuber yield and quality of Jerusalem artichoke in a semi-arid environment.