In this paper, we have applied Spectrally Modulated Spectrally Encoded (SMSE) framework to design multiple input multiple output (MIMO) waveform. The existing SMSE framework can be used to generate different multi-carrier waveforms by appropriately designing variables including data, coding, orthogonality, windowing, availability of frequency and used frequency components. It has been approved to be a generic framework to generate multi-carrier waveforms for cognitive radio due to its flexibility. However, spacial diversity has not been considered in the framework. Hence, we extend the SMSE framework with MIMO capability in this paper. Simulation results prove the spacial diversity gain of SMSE-based MIMO waveform. The SMSE-based MIMO waveform design can be applied in cognitive radio to improve transmission rate and in radar to improve radar performance.