The invention relates to low-carbon high-strength Cr-containing nanoscale bainite steel and a preparation method thereof. The preparation method comprises the following steps: carrying out billet rolling to prepare a plate, heating the plate at the heating rate of 5-10 DEG C/s to 980-1020 DEG C, carrying out thermal insulation for 10-20 min, water-cooling to 410-430 DEG C, air-cooling to 340-360 DEG C, carrying out thermal insulation for 10-20 min, and water-cooling to room temperature to prepare the low-carbon high-strength Cr-containing nanoscale bainite steel. The billet contains the following chemical components (by weight): 0.23-0.25% of C, 1.70-1.93% of Si, 1.98-2.02% of Mn, 0.227-0.230% of Mo, 0.98-1.02% of Cr, P being less than 0.008%, S being less than 0.002%, N being less than 0.004%, and the rest of Fe and unavoidable impurities. The preparation method of the invention has characteristics of low cost, short period and simple process. The prepared low-carbon high-strength Cr-containing nanoscale bainite steel has excellent mechanical property and is widely applied in fields of engineering machinery, maritime facilities, bridge, automobile, shipbuilding, pressure vessel, etc.