We describe the orientation, number, size, distribution, and fracture spatial arrangement in the central part of the kilometric Tuxtla-Malpaso fault system, one of the largest in the south of Mexico which cuts Cretaceous calcareous rocks. In this area, there are two sub-vertical extensional fracture sets (T1 and T2). The T1 fractures have ∼ N–S orientation and recorded 4.48 % of extension. The T2 fractures cut the T1 fractures, have NE-SW orientation, and accommodate an amount of extension of 3.87 %. These two fracture sets are parallel to two normal fault groups. The youngest normal faults (F2) have NE-SW strike and cut the N–S normal faults (F1). The F1 faults record a reactivation as strike-slip faults contemporaneous with F2.The T1 and T2 fractures have a fracture intensity between 9.08 and 9.39 (P10) on mesoscopic scale. In the case of the spacing, the value of this parameter (0.28–1) is related to fracture clustering. This behavior agrees with the values of fractal box dimension (0.72–0.81), correlation dimension (0.24–0.6), Lyapunov exponent (1.31–2.42), and coefficient of variation (0.94–1.85) on mesoscopic scale. The cumulative aperture vs. distance shows that T1 and T2 fractures have heterogeneous strain distribution. The fracture spatial arrangement is verified with the normalized correlation count analysis (NCC). The NCC graphs show a clustering behavior for T1 and T2 fractures, which are related to a regulary-spaced fractal clusters pattern. We suggest that this pattern is related to the mechanical stratigraphy and the strain location in the fault zones, while the fracture intensity depends on the degree of fracture clustering and rock type more than the amount of strain.Finally, the T1 fractures were associated with the right strike-slip kinematic for the NW-SE Tuxtla-Malpaso fault. This activity recorded a transtension behavior during the middle Miocene. The T2 fractures were formed during the reactivation (Pliocene) of the Tuxtla-Malpaso fault as the left strike-slip fault behind wrenching-transpression kinematics.