It has been confirmed that silicon (Si) fertilizer and humic acid (HA) could effectively decrease the heavy metals in soil. Nonetheless, the impact of these additives on soil aggregate characteristics was ignored. Therefore, the effects of Si fertilizer, HA, and their combinations on the physicochemical characteristics, availability of heavy metals (Cu, Cd, Pb, Zn), and fraction changes in soils and soil aggregates were investigated in this research. The results showed that Si fertilizer and HA significantly modified soil properties such as soil pH, electrical conductivity total organic carbon, water-soluble organic carbon, and nitrate‑nitrogen. HA and Si-HA (SHA) supplementation significantly decreased the availability of Cu, Cd, Pd, and Zn. Besides, there was no significant difference in physicochemical properties between soil and soil aggregates. The availability of Cu, Cd, Pd, and Zn in soil aggregates could be significantly inhibited by the addition of HA and SHA, and the content in microaggregates was greater than that in macroaggregates. After the addition of the three additives, the main fractions of heavy metals in different particle sizes were changed and eventually transformed to the residue state. These results indicated that Si fertilizer, HA, and SHA were influential in physicochemical properties and metal availability in soil aggregates. Therefore, it is of great scientific significance to study the impact of heavy metal pollution on the ecological environment in different aggregates, which will provide reference data for future sustainable management of heavy-metal polluted soils.