Multifunctional semiconductors play an important role in developing advanced photoelectric technologies. In this work, based on an octahedral replacement strategy in chalcogenides, a new selenide semiconductor NaMn3Ga3Se8 was rationally designed, and synthesized by the flux method. The compound crystallizes in the noncentrosymmetric (NCS) P-6 space group, and is composed of unique prismatic [NaSe6], octahedral [MnSe6] and tetrahedral [GaSe4] motifs, inheriting the stable three-dimensional framework built by the octahedral and tetrahedral units in the  A^IMg₃^IIC₃^IIIQ₈^VI family. NaMn3Ga3Se8 shows the largest known secondary nonlinear optical (NLO) response of ∼2.1 × AgGaS2 (AGS) in the A^IMg₃^IIC₃^IIIQ₈^VI family, and a high laser-induced damage threshold of ∼3.0 × AGS. Meanwhile, the introduction of Mn2+ with unpaired 3d electrons induces a strong red emission band (685–805 nm) under the excitation source of 496 nm, as well as a paramagnetic to antiferromagnetic (AFM) transition at 7.3 K. The results confirm that NaMn3Ga3Se8 possesses multifunctional features including significant NLO response, fluorescence emission and AFM properties, and illustrate that replacing octahedral units with approaching size and geometry (like [MgSe6] and [MnSe6]) could be a feasible way to develop multifunctional chalcogenides.