Friction and contact characteristics play important roles in brake squeal generation, while their heterogeneous characteristics are often neglected. In this paper, a flexible pin-on-disc system model is established. Squeal bench test is carried out to verify the correctness of the model. Random heterogeneous friction coefficients and contact stiffnesses are built and assigned to the model. Evaluation indexes of friction and contact heterogeneities are established. The unstable region and the squeal uncertainty are analyzed. Then, the influence of the heterogeneous friction and contact characteristics on generation of brake squeal is explored based on statistical method and uncertainty concept in the unstable region and the mix region respectively. The results show that when only friction coefficient is heterogeneous, the radius of the center position of friction coefficient is the key influencing factor of brake squeal; when only contact stiffness is heterogeneous, the radius of the center position of contact stiffness is the key influencing factor of brake squeal; when friction coefficient and contact stiffness are both heterogeneous, the mean value of the product of friction coefficient and contact stiffness and the radius of the center position of friction coefficient play critical roles on friction squeal. Besides, squeal tends to occur when the mean value of the product of heterogeneous friction coefficient and contact stiffness and the radius of the center position of friction coefficient are large.