This study addresses the challenge of cognitive waveform design for multiple-input–multiple-output (MIMO) radar systems operating in cluttered environments. It focuses on the key practical requirements for transmitting time-domain waveforms and proposes a novel approach. This method first determines the optimal frequency-domain waveform and then designs a time-domain waveform that closely approximates the frequency-domain solution. The primary objective is to enable MIMO radar systems to transmit orthogonal waveforms while accommodating various constraints. A frequency-domain waveform optimization model was initially developed using the principle of maximizing dual mutual information (DMI), and the energy spectral density (ESD) of the optimal waveform was derived using the water-filling method. Next, a time-domain waveform approximation model is constructed based on the minimum mean square error (MMSE) criterion, which incorporates constant modulus and peak-to-average power ratio (PAPR) constraints. To minimize the performance degradation of the waveform, an improved adaptive gradient descent genetic algorithm (GD-AGA) was proposed to synthesize multichannel orthogonal time-domain waveforms for MIMO radars. The simulation results demonstrate the effectiveness of the proposed model for enhancing the performance of MIMO radar. Compared with traditional genetic algorithms (GA) and two enhanced GA alternatives, the proposed algorithm achieves a lower ESD loss and better orthogonal performance.