For the inadequate interlaminar strength of 2D carbon/carbon (C/C) composite, in-situ grown carbon nanotubes (CNTs) reinforcing strategy was put forward to strengthen the interlaminar matrix at the nanoscale and inhibit the interlaminar cracking. CNT morphology is an essential factor in influencing the enhancement effect. Herein, the influence of in-situ grown CNT morphology on the microstructure and mechanical properties of C/C composite was deeply studied. The radially-aligned straight CNTs could induce the formation of highly-ordered pyrolytic carbon (PyC), while PyC in randomly-distributed curved CNTs concentrated area exhibits an isotropic structure. Further, radially-aligned straight CNTs show better improvement on the flexural and shear strength of C/C composites. According to the fine structural characterization and finite element simulation, the influence mechanism of CNT morphology was revealed. CNT morphology can influence the stress distribution in the PyC protective layer, and compared with radially-aligned straight CNTs, randomly-distributed curved CNTs induce higher tensile stress in the PyC protective layer, which has a detrimental impact on the flexural and shear properties of C/C composite. This work provides novel insights into the effect of CNT morphology on the microstructure and mechanical properties of C/C composites, which gives a basis for the structural design and preparation of CNTs reinforced C/C composites.