In the ultra-tight integration, the signal processing of GNSS receiver baseband can be enhanced by the aiding of INS information. With the purpose of improving the performance of ultra-tight integration with low-cost MEMS (Micro-Electro-Mechanical System) IMU (Inertial Measurement Unit), the paper explores a deeply coupled integration scheme of GNSS and the software defined IMU (SDI) based on vibratory MEMS rate gyroscope. The error of vibratory MEMS rate gyroscope demodulated by peak detection technique is interpreted in the gyroscope signal domain and the gyroscope demodulation parameter deviations are estimated by the integration filter and adjusted accordingly. The presented integration scheme is tested by an integrated navigation system which consists of a software defined GNSS receiver, a single-axis vibratory MEMS gyroscope GI-CVG-N2100A based SDI and an Xsens MEMS IMU. The single-axis vibratory MEMS gyroscope GI-CVG-N2100A in the test, is employed to replace one of the gyroscope axes of the Xsens MEMS IMU.