The recent research show that low melting temperature alloys (LMA) is a prospective thermal interface material (TIM). However, the effect of surface roughness and interface contact pressure on the thermal contact resistance with LMA as TIM is unclear. In the current research, copper plates with surface roughness of 0.28 μm, 0.54 μm, 0.96 μm and 2.59 μm were fabricated to make different test samples. Low melting temperature alloys Ga62.5In21.5Sn16 was used as TIM to make the Cu-LMA-Cu three-layer structure samples. The thermal contact resistance of these samples under different pressure of 0.05 MPa, 0.1 MPa, 0.15 MPa, 0.2 MPa, 0.4 MPa and 0.6 MPa were measured based on the steady state method. The results show that when the pressure of 0.05 MPa, 0.1 MPa, 0.15 MPa, 0.2 MPa, 0.4 MPa, 0.6MPa is applied to the samples, the thermal contact resistance of sample with surface roughness of 0.28 μm decreased by 74.3%, 71.1%, 70.1%, 71.5%, 70.8%, 70.1% compared with that of the sample with surface roughness of 2.59 μm. In order to further study the influence of the factors on the thermal contact resistance, a theoretical model of solid-liquid-solid thermal contact resistance with contact pressure and surface roughness as factors was developed. Based on theoretical model, it is concluded that (1) the thermal contact resistance decreases as the pressure increases, and gradually stabilizes; (2) as the surface roughness increases, the thermal contact resistance increases; (3) As the surface roughness decreases, the influence of contact pressure on thermal contact resistance decreases. The above conclusions were verified by test results.