The synthesis of high ductility geopolymer composites using excavated natural clay is an economical and environmentally friendly method to realize the utilization of excavated natural clay. This paper presents an experimental research on the flexural properties and pore structure characteristics of engineered geopolymer composites (EGC) prepared by calcined natural clay. The EGC with different slag and fiber contents were prepared and the four-point bending tests were conducted on the EGC. The effect of slag and fiber content on the flexural strength, flexural deflection and flexural toughness were discussed. The microscopic pore structure characteristics of EGC were further analyzed. The optimal mixture ratio of calcined clay-based EGC with the highest flexural toughness was proposed. The results show that fiber can significantly enhance the flexural properties and cracking control ability of EGC. The ultimate flexural strength, flexural deflection, flexural strengthening index and flexural toughness of EGC all increase with increasing fiber content. The results also show the addition of 10.0% slag can increase the flexural strength and flexural toughness, while excessive slag content reduces the flexural properties. The EGC with 10.0% slag content and 2.5% fiber content exhibits excellent flexural properties and cracking control ability. The ultimate flexural strength and flexural toughness index reach 9.75 MPa and 486.11, showing the highest flexural toughness.