Thin-walled parts refer to lightweight structural parts comprised of thin plates and stiffeners. During the machining process of thin-walled parts, machining distortion often occurs due to uncertain factors such as varying stiffness, cutting force, cutting temperature, residual stress and other factors. This paper studied the minimization of the failure probability of machining distortion by controlling the uncertainties of inputs. For this, a fuzzy inference model for the machining system was proposed to determine the effects of uncertain factors on the machining distortion errors, which was composed of rule frame and result frame. In the rule frame, machining parameters, outline size, and wall thickness were used as inputs. In the result frame, linear stiffness, cutter path, as well as cutting force were taken as the input parameters. The values of machining distortion were the output, taken into a threshold function. Comprehensive matching was defined to measure the importance of uncertain inputs to outputs. Machining distortion will exceed the specification (failure) with the increase in comprehensive matching. Therefore, the comprehensive matching index evaluates the effects of the uncertainties on the machining distortion and quantify the effects of given uncertain parameters. Two engineering examples were employed to illustrate the accuracy and efficiency of the proposed approach. It revealed that the comprehensive matching of cutting force to the failure probability of machining distortion was the maximum, 0.040, which was 12 to 13 times greater than that of linear stiffness or cutter path.