Space-based early warning radar faces significant challenges due to its extensive detection ranges and high operational speeds, leading to substantial range and Doppler ambiguities. In addition, the Earth's rotation contributes to radar clutter exhibiting a pronounced range dependence, causing clutter signals from various ambiguous range regions to spread across different Doppler frequencies. This complexity greatly diminishes the effectiveness of conventional space-time adaptive processing (STAP) in clutter suppression. In response, an element pulse coding (EPC)-frequency diverse array (FDA)-multiple input multiple output (MIMO) radar has been proposed. This radar uses azimuth EPC to substantially reduce pitch sidelobe signals, followed by pitch FDA for further suppression of residual pitch sidelobes, thus effectively isolating the pitch mainlobe signal. STAP is subsequently employed to suppress the remaining clutter. However, a significant challenge for this radar is the need to transmit thousands of different waveforms, which are required to be mutually orthogonal, and hard to achieve in practice. Therefore, this article introduces improvements to the EPC-FDA-MIMO radar. We have altered the radar's signal transmission mode, transitioning from the original method of simultaneous transmission by the full array to a more efficient time-sliding window subarray transmission. This adjustment not only increases the signal power but also reduces the number of orthogonal waveforms necessary for transmission. Furthermore, we have conducted a thorough study and analysis of the signal model and clutter suppression capabilities of the EPC-FDA-MIMO radar when operating with nonorthogonal waveforms. A method to enhance waveform orthogonality has been developed and is presented in this article. This method effectively minimizes the adverse effects of nonorthogonal waveforms on the radar's performance. Theoretical analysis and simulation experiments are included, demonstrating the efficacy of these proposed methods.