In the modern pile foundation drilling operation, a series of regular joints will be left on the rock surface during the serration rotation of the drill, and the traditional method to determine the roughness of the joint has great limitations. For more accurately quantify the roughness of rock joint under the condition of rotary drilling, the geometry of rock joint surface is obtained by three-dimensional non-contact high-precision laser scanner. Twenty contours of the joint surface were intercepted along the shear direction on the XZ system plan. The mean height h0 and RMS σ of the center line reflecting the undulation characteristics of the joint surface and the parameter θp reflecting the steepness of the joint surface are extracted by using the contour lines. The method of quantizing roughness with L/L0 is extended to three-dimensional space S/S0, the functional relation between JRC and σ and θp is obtained by bivariate fitting, and the goodness of fit reaches 99.46%. The results of two real examples and laboratory direct shear tests show that the proposed method is close to other methods, and the numerical variation trend is more stable than that of the classical method, which verifies the feasibility of the proposed method.