In this paper, aligned multi-walled carbon nanotubes (A-MWNT) and non-aligned multi-walled carbon nanotubes(MWNT) of different volume fractions were dispersed into natural rubber (NR) via solution blending, and subsequently NR nano-composites were prepared through ambient cross-linking. Then the dispersions of A-MWNT and MWNT in rubber matrix were observed, and the effects of A-MWNT and MWNT on the glass transition temperature (T_g) of rubber composites, cross-linking heat release under high temperature and heat conduction performances were analyzed. Research showed that parts of the A-MWNT would be disorganized in the process of solution blending, ultrasonic oscillation and stir, be aligned in micro-area units but isotropic on the whole. As the fraction of A-MWNT increased, T_g gradually decreased then increased, heat release under high temperature gradually increased. Compared with composite materials filled with MWNT in the same condition, the thermal conductivity of the composites filled with A-MWNT increased quickly with the enhancement of A-MWNT fraction, jumping to maximum of 0.735 W/(mK) when filled with 10% A-MWNT, which was increased by 222.4%.