The effect of a complex additive consisting of silica fume and enrichment waste from the Karagailinsky mining and processing plant on the hydration and structure formation processes of cement systems is investigated. It was established that the introduction of a complex modifying additive consisting of silica fume and enrichment waste from the Karagailinsky mining and processing plant into the cement composition CEM I 42.5 N SR increases the compressive strength at the age of 28 days by 15.7–28 %. It was revealed that the studied complex additives contribute to an increase in the amount of chemically bound water. The processes of hydration and hardening of multicomponent modified binders were investigated. It is shown that the high strength of cement stone on a modified binder is due to the formation of stable low-base hydro silicates. The source of the formation of low-base calcium hydro silicates is the pozzolanic reaction, which proceeds with the binding of the clinker minerals released during hydration, portlandite silica complex additive. It is shown that purposefully changing the composition of the binder and hydration conditions, it is possible to improve the phase composition, morphology of hydrates and influence its final properties.