The marine silicon cycle is one of the key biogeochemical cycles in the marine realm. It can regulate the global atmospheric carbon dioxide concentration and seawater pH, and also plays a significant role in the geochemical cycles of many other elements, including nitrogen (N), phosphorus (P), iron (Fe) and aluminum (Al). The closely intertwined coupling relationships between the marine silicon cycle and “biological pump” as well as the carbon cycle have caused for substantial concerns under the looming threat of global climate change and increased anthropogenic influences. Silicon (Si) is transported into the ocean through rivers, submarine groundwater, atmospheric deposition, basalt weathering and hydrothermal vents, however, subpolar glaciers are becoming an important Si source to the high latitude ocean regions due to global warming. And Si is removed from the ocean through biogenic silica (bSi) deposition, silicious sponges and bSi reverse weathering. The marine silica cycle involves complex biological (organism-mediated absorption/degradation), physical (adsorption, dissolution) and chemical (mineralization, reverse weathering) processes, while studying these processes could strengthen our understanding of its “source-sink” and the silica budget. This study reviews the major processes and challenges in the marine silica cycle, re-evaluates the marine silica budget based on recent advances, and indicates the major scientific questions for future works. Current works indicated that the input and output fluxes of marine Si have increased 2.4 and 2.2 times, respectively, than the previous estimates. On a short geological time scale (< 8 ka), the total Si net inputs are approximately balanced by the total Si net output flux; therefore, the modern ocean Si cycle is generally at steady state. Nonetheless, the input fluxes of Si to marginal seas through rivers can be influenced by the climate change and human activities, which can then affect the structures of phytoplankton community, including diatoms. This issue is one of the major issues in the marine silicon cycle and requires further research in the future. The coastal and continental margin zones (CCMZ) are oceanic regions with characteristics of high sedimentation rate and rapid reverse weathering, where the bSi burial fluxes is still difficult to estimate accurately. Present studies have assessed the bSi production rates for planktonic diatoms, silicious sponges and rhizaria, but the role of benthic diatom in bSi production was ignored. This omission should be addresses in the future study of benthic diatom primary production and its role in the marine silicon cycle.