Inertial Navigation System (INS) is one of the navigation systems widely used in various land-based, aerial, and marine applications. Among all types of INS, Microelectromechanical System (MEMS)-based INS can be widely utilized, owing to their low cost, lightweight, and small size. However, due to the manufacturing technology, MEMS-based INS suffers from deterministic and stochastic errors, which increase positioning errors over Time. In this paper, a new effective noise reduction method is proposed that can provide more accurate outputs of MEMS-based inertial sensors. The intelligent method in this paper is a combined denoising method that combines Wavelet Transform (WT), Permutation Entropy (PE), Support Vector Regression (SVR), and Genetic Algorithm (GA). Firstly, WT is employed to obtain a Time-frequency representation of raw data. Secondly, a four-element feature vector is formed. These four features are (1) amplitude of frequency, (2) its ratio to mean of amplitudes of all frequencies, (3) location of frequency in Time-frequency representation, and (4) judgment on behaviors of frequency that is obtained by utilizing PE. Thirdly, based on the feature vector, the GA-SVR algorithm predicts amplitudes of all frequencies in the Time-frequency representation of the denoised signal. Finally, by employing inverse WT the denoised signal is obtained. In this work, the outputs of the Inertial Measurement Unit (IMU) in ADIS16407 sensor, as a low-cost and MEMS-based INS, have been utilized for data collection. The proposed method has been compared with other noise reduction methods and the achieved results verify superior improvement than other methods.