Multilayer cBN/NCD (cubic boron nitride and nano-crystalline diamond) composite coating with modulation periods of 1 μm, 1.5 μm and 3 μm were deposited by anode layer linear ion source assisted radio frequency magnetron sputtering (ALLIS-RFMS) and microwave plasma chemical vapor deposition(MPCVD) on cemented tungsten tools (YG6) and Si substrates. The microstructures, mechanical and tribological properties of the multilayer composite coating were systematically characterized and investigated. In this work, with a decrease of modulation periods, the surface roughness of cBN/NCD multilayer composite coatings exhibited an increasing trend, but the mechanical properties were improved significantly. When the modulation period decreases to 1 μm, the residual stress of the composite coating can be reduced to −0.61 GPa, fracture toughness increased to 4.81 MPa⋅m1/2. Friction and wear tests demonstrated that the wear resistance of the multilayer cBN/NCD composite coating was related to the residual stress and fracture toughness, the friction coefficient keep a stable values about 0.12– 0.15, the wear rate decreased significantly with decreasing modulation period, and the lowest wear rate was about 3.69 × 10−6 mm3/(N⋅m) when the modulation period is 1 μm. The work suggests that decreasing the modulation period is an effective way to improve the mechanical and tribological properties of multilayer cBN/NCD composite coating.