A CNOT gate is an important quantum component for quantum computation, which is widely used in fault-tolerant extended-rectangle construction. However, the ancilla state preparation circuit is normally complicated in the construction of fault-tolerant extended-rectangle for quantum CNOT gates, which brings inconvenience in the design and implementation. A novel construction of fault-tolerant quantum CNOT gates using (49,1,9) quantum code is presented using overlap method to simplify the encoded ancilla preparation state circuit. The result shows that the construction is optimized and the number of CNOT gates needed is 224 less than that with the traditional Latin rectangle method.