The geopolymer mortar (GPM) prepared from industrial by-products and alkali activation solution (AAS) is one of the hot spots of current building materials. As a feasible alternative to natural river sand, manufactured sand (MS) alleviates the global ecological pressure. In this study, MS was used for fine aggregate. Sodium hydroxide (NaOH) and sodium silicate (Na2SiO3) solution were used as AAS. Metakaolin (MK) and fly ash (FA) were used as the precursor to prepare MK-FA-based GPM with MS (MS-GPM), which was of great significance for saving non-renewable resources, mitigating the greenhouse effect, and recycling waste. Numerous studies were conducted to explore the effect of sand–precursor ratio (r
sp) on mechanical and durability characteristics of MS-GPM. Relationships between compressive strength and tensile or flexural strength were established by linear fitting equation. Finally, analysis of variance (ANOVA) was used to systematically calculate the effect of r
sp on performance. The results indicated that the mechanical strength and impermeability of MS-GPM decreased and crack resistance increased with r
sp from 1 to 5. The strength of MS-GPM was the best when r
sp was 1. With the increase of r
sp, the proportion of MS in MS-GPM increases, and the relative cementitious material decreases, which has an adverse impact on mechanical properties and impermeability. Linear fitting revealed that the compressive strength of MS-GPM was closely related to tensile strength and flexural strength. ANOVA results indicated that r
sp in the range of 1–5 had great effects on the performance of MS-GPM. The aim of this article is to further promote the possibility of applying MS-GPM in practical engineering by designing reasonable r
sp.