In this paper, a novel multiple input/multiple output (MIMO) antenna system with a graphene-based patch antenna arrays for THz communications channel capacity enhancement has been proposed and investigated. Systematic analysis has been conducted on the graphene load conductivity by determining the operating modes related to its chemical potential. Further, the projected MIMO antenna arrays have been designed with three different approaches such as homogeneous, photonic crystals and optimized photonic crystals. The targeted MIMO antenna arrays have been compared with their radiation characteristics such as return loss, bandwidth and gain. The obtained results in CST simulations of the proposed graphene-based 1×2 patch antenna array using optimized photonic crystals substrate exhibited excellent performance improvement as compared to the homogeneous substrate and photonic crystals substrate around 0.65 THz, which achieved a peak gain of 11.80 dB and broad bandwidth greater than 614 GHz. Next, The 2x2 MIMO system scenario was studied and analyzed using the mentioned targeted MIMO antenna arrays by calculating the total path loss and the channel capacity. The obtained results showed that the proposed 2x2 MIMO system with MIMO antenna array based on the optimized photonic crystals substrate achieved the highest capacity and the lowest total loss compared to a simple MIMO antenna array based on a homogeneous substrate. The capacity was calculated as 23.64 bit/s/Hz, and this was a remarkable enhancement compared with previously reported studies. In addition, this capacity was investigated further for different system configurations and different spacings between the transmission antennas and receiver antennas.