The anisotropy of mechanical properties of hard rocks is usually affected by the internal primary hidden microfissure structures, which tend to induce secondary rock fracture propagation even surrounding rock instabilities in deep underground excavation. This research attempts to reveal the control effect of primary hidden microfissures on the mechanical behaviors and failure characteristics of cryptocrystalline basalt with hidden microfissures (CBWHM) through a series of laboratory tests. Firstly, a geometric feature extraction method for primary hidden microfissures of basalt rock has been proposed, by which 20 groups of three-dimensional (3D) visualization models of cylindrical basalt samples were established, and the distribution location and volume crack rate (KV) of hidden microfissures were simultaneously determined. On this basis, a series of the uniaxial compression tests of basalt samples with synchronous acoustic emission (AE) were carried out. Results show that the location and development degree of primary hidden microfissures significantly control the mechanical characteristics of basalt, with the relevant micro-fracture events occurring earlier and throughout the whole loading process compared with intact samples. In general, there exists a uniaxial polynomial fitting relationship between the strength of basalt samples and KV. The larger the KV, the lower the peak strength (σc) of basalt, which could decrease by 30–50% compared to that of the intact rock when KV is more than 5‰. However, when the hidden microfissures with large dip angles are located close to the central axis, the influence of KV on the rock strength becomes less, but the crack propagation and failure morphology are still obviously controlled by the hidden microfissures. The statistical analysis results of surface cracks and rock fragment characteristics of the damaged basalt samples further show that the basalt rock is easy to expand, penetrate and eventually fail along the hidden microfissures under loading, and it is tensile fracture that controls the failure of CBWHM. With an increase of KV, the mass percentage (W) of the coarse particle of the sample fragments increases gradually, and the fractal dimension (D) of the rock fragments and KV of the hidden microfisures show an obvious logarithmic curve relationship. The research could provide effective guidance for the interpretation of the meso-mechanism of hard rock failures.