The Spartina alterniflora started to invade the Min River estuary (Southeast China) in 2002 and, thereafter, its invasion area showed an increasing trend. Since the siltation depths caused by S. alterniflora in the Min River estuary were much higher (4.8–7.2 cm yr−1) than the values reported in other coastal regions of China (3.5–6.5 cm yr−1), the impacts of siltation on nutrient cycle processes in this region might be more evident. In order to explore the potential effects of siltation by S. alterniflora on nutrient ((carbon (C), nitrogen (N), phosphorous (P) and sulfur (S)) variations in its decaying litters, three one-off siltation treatments (no siltation scenario (0 cm yr−1, NSS), current siltation scenario (5 cm yr−1, CSS) and strong siltation scenario (10 cm yr−1, SSS)) were designed in coastal marsh of the Min River estuary and the in-situ decomposition experiment was conducted from February 2016 to February 2017 by litterbag technique. Results showed that the siltation caused by S. alterniflora showed significant impact on its decomposition rate, following the sequence of NSS (0.005638 d−1) > SSS (0.003005 d−1) > CSS (0.002478 d−1) (p < 0.05). The total carbon (TC) contents in decomposing litters in the three siltation treatments showed dissimilar fluctuations and significantly higher values were observed in the CSS and SSS treatments compared to the NSS treatment. The contents of total nitrogen (TN) and total sulfur (TS) in decomposing detritus in the three siltation treatments generally showed increasing trend during the whole decomposition, while those of total phosphorus (TP) showed increasing trend after decomposing for 30 days. The differences in nutrient variations among the three siltation treatments, to a great extent, rested with the alterations of substrate quality in detritus during the experiment. Although the stocks of C, N, P and S in detritus in the three siltation treatments evidenced the release from litters to the surroundings during decomposition, the release amounts of these nutrients in some periods were at a lower level. With increasing siltation depths, the release of C, N and P from detritus was generally restrained during the whole decomposition, while that of S from decaying litters was inhibited only at the late stage of decomposition. This paper found that the siltation caused by S. alterniflora reduced the nutrient return (particularly for C, N and P) from its detritus, which, in turn, might greatly alter the nutrient cycle in S. alterniflora marsh.