Alkali activated slag (AAS) mortar is becoming an increasingly popular green building material because of its excellent engineering properties and low CO2 emissions, promising to replace ordinary Portland cement (OPC) mortar. However, AAS’s high shrinkage and short setting time are the important reasons to limit its wide application in engineering. This paper was conducted to investigate the effect of internal curing(IC) by super absorbent polymer (SAP) on the autogenous shrinkage of AAS mortars. For this, an experimental study was carried out to evaluate the effect of SAP dosage on the setting time, autogenous shrinkage, compressive strength, microstructure, and pore structure. The SAP were incorporated at different dosage of 0, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 percent by weight of slag. The workability, physical (porosity), mechanical, and shrinkage properties of the mortars were evaluated, and a complementary study on microstructure was made. The results indicated that the setting time increased with an increase of SAP dosage due to the additional activator released by SAP. Autogenous shrinkage decreased with an increase of SAP dosage, and was mitigated completely when the dosage of SAP ≥ 0.2% wt of slag. Although IC by means of SAP reduced the compressive strength, this reduction (23% at 56 days for 0.2% SAP) was acceptable given the important role that it played on mitigating autogenous shrinkage. In the research, the 0.2% SAP dosage was the optimal content. The results can provide data and basis for practical application of AAS mortar.