From April 2008 to November 2009, a field decomposition experiment was conducted to investigate the effects of sediment burial on macro (C, N) and microelement (Pb, Cr, Cu, Zn, Ni, and Mn) variations in decomposing litter of Phragmites australis in the coastal marsh of the Yellow River estuary. Three one-off sediment burial treatments [no sediment burial (0 mm year(-1), S0), current sediment burial (100 mm year(-1), S10), and strong sediment burial (200 mm year(-1), S20)] were laid in different decomposition sites. Results showed that sediment burials showed significant influence on the decomposition rate of P. australis, in the order of S10 (0.001990 day(-1)) ≈ S20 (0.001710 day(-1)) > S0 (0.000768 day(-1)) (p < 0.05). The macro and microelement in decomposing litters of the three burial depths exhibited different temporal variations except for Cu, Zn, and Ni. No significant differences in C, N, Pb, Cr, Zn, and Mn concentrations were observed among the three burial treatments except for Cu and Ni (p > 0.05). With increasing burial depth, N, Cr, Cu, Ni, and Mn concentrations generally increased, while C, Pb, and Zn concentrations varied insignificantly. Sediment burial was favorable for C and N release from P. australis, and, with increasing burial depth, the C release from litter significantly increased, and the N in litter shifted from accumulation to release. With a few exceptions, Pb, Cr, Zn, and Mn stocks in P. australis in the three treatments evidenced the export of metals from litter to environment, and, with increasing burial depth, the export amounts increased greatly. Stocks of Cu and Ni in P. australis in the S10 and S20 treatments were generally positive, evidencing incorporation of the two metals in most sampling times. Except for Ni, the variations of C, N, Pb, Cr, Cu, Zn, and Mn stocks in P. australis in the S10 and S20 treatments were approximated, indicating that the strong burial episodes (S20) occurred in P. australis marsh in the future would have little influence on the stocks of these elements. With increasing burial depths, the P. australis was particularly efficient in binding Cu and Ni and releasing C, N, Pb, Cr, Zn, and Mn, implying that the potential eco-toxic risk of Pb, Cr, Zn, and Mn exposure might be very serious. This study emphasized the effects of different burials on nutrient and metal cycling and mass balance in the P. australis marsh of the Yellow River estuary.