His key research areas include: biogeochemical cycling of carbon and nutrients in terrestrial ecosystems, soil carbon sequestration, soil quality and health, drought mitigation, nutrient pollutant tracing in reef, restoration of degraded ecosystems, microplastic in agroecosystems and waste (organic and plastic) recycling.

Prof Chen has secured over $20 million of external competitive funding as a lead CI or co-CI in the past ten years (2014-2024), with current funding of > $10M for next 5 years (2024-2029). The majority (ca.50%) of this funding came from ARC (including 1 ARC Future Fellowship, 4 ARC Discovery grants, 3 ARC Linkage grants and 2 ARC LIEF grants) and ca. 50% from government agencies and industry (e.g., ACIAR, SRA, NESP, QLD Water Infrastructure, DPI NSW, Alcoa).