In the coal-rock system, the interlayer weak zone between coal and rock layers is the primary area of fracture distribution. These fractures penetrate the coal and rock layers, seriously impacting the mechanical properties and engineering stability of the coal-rock system. To investigate the impact of penetrating fractures on the mechanical properties of the coal-rock system, axial loading tests were conducted on prefabricated coal-rock composite bodies with five different fracture lengths and angles. The findings indicate that: 1) As the fracture length increases, the compressive strength, elastic modulus, peak energy, and impact energy index decrease linearly. Regarding the fracture angle, the compressive strength, elastic modulus, peak energy, and impact energy index initially decrease and then increase. 2) The destructive acoustic emission tests of the samples exhibit three stages: a quiet period, an active period, and an intense period, respectively. With increasing fracture length, the cumulative energy of acoustic emission initially increases and then decreases. Similarly, with increasing fracture angle, both peak energy and cumulative energy of acoustic emission first increase and then decrease. 3) The length and angle of fracture have a certain influence on the wing crack, secondary inclined crack, secondary coplanar crack, oblique crack, secondary derivative crack, wing crack derivative crack, far field crack and spalling phenomenon. 4) As fracture length increases, the cohesion and internal friction gradually decrease, while an increase in fracture angle leads to a decrease followed by an increase in cohesion and internal friction. 5) The Drucker-Prager strength criterion considering fracture length and angle was developed, and rationality verification indicated a sample error within a reasonable range of 1.367% to 5.055%. 6) Based on the dissipative structure theory, the study analyzed the mechanism of instability failure in the coal-rock combined body. The failure process of the combined body involved four main stages: quasi-steady state, metastable state, instability, and establishment of a new steady state. An energy migration model for the fractured coal-rock combined body was developed, and the energy migration pattern during the instability and failure of the fractured coal-rock combined body was analyzed. The ends of the fracture were identified as the primary areas of energy accumulation. Destruction of the coal component’s fracture end led to the migration of energy towards the fracture end of the rock component, resulting in the release of energy through rock component destruction or deformation. These research findings offer valuable insights for investigating the mechanical characteristics of deep coal and rock, as well as understanding the mechanisms behind dynamic coal and rock disasters.