Semiconductor photocatalysis has been regarded as an environmentally friendly technology in wastewater treatment and energy production. Here, a series of direct Z-scheme MnIn2S4/g-C3N4 (MnISCN) photocatalysts without electron mediators were fabricated by a simple hydrothermal route on the basis of in-situ loading of MnIn2S4 (MnIS) nanoflakes on the surface of g-C3N4 (CN) nanosheets. Photocatalytic performances evaluated under visible light irradiation revealed these Z-scheme heterostructured photocatalysts exhibited higher photocatalytic activities than single-component samples. The effect of weight ratio between MnIn2S4 nanoflakes and mesoporous CN nanosheets on photocatalytic activity towards treatment of pharmaceutical wastewater was optimized to achieve highly efficient photocatalytic activities for both degradation of pharmaceutical wastewater and hydrogen generation compared with alone MnIS nanoflakes and isolated mesoporous CN nanosheets. The significant enhancement in photocatalytic activity could be primarily ascribed to the construction of Z-scheme MnISCN architectures, which effectively accelerated the transfer and separation of photogenerated charge carriers via tight interface contacts built among these two components. The recycling experiments for pharmaceutical wastewater treatment revealed the excellent stability of MnISCN nanocomposites. The advantages of highly efficient photocatalytic activity and excellent stability endowed a promising potential for MnISCN nanocomposites to apply in photocatalytic fields.