A high-precision time reference is fundamental to the positioning, navigation, and timing (PNT) of global navigation satellite systems (GNSS). The precision of clock steering determines the accuracy of practical applications that rely on the time–frequency reference. With the invention of direct digital synthesizer (DDS) technology, digital clock steering (DCS) has gradually become a mainstream technology. However, the key factor limiting DCS accuracy is the system quantization noise, which leads to a low frequency and phase adjustment accuracy. Here we propose a DCS method based on Σ-Δ modulation to address the issue of low resolution of DAC through shaping the quantization noise. A simulated GNSS time–frequency reference system experimental platform is constructed to validate the effectiveness of the proposed method. The experimental results demonstrate that this method achieves a phase adjustment accuracy of 0.48 ps and a frequency adjustment accuracy better than 0.48 pHz, which is two orders of magnitude higher than that of existing GNSS time–frequency reference systems. Thus, the proposed method offers a significant improvement in time–frequency reference systems, leading to better performance, reliability, and accuracy in a wide range of practical applications.