Headwater streams have low productivity and are closely linked to forest ecosystems, which input a large amount of plant litter into streams. Most current studies have focused on the decomposition process of plant litter in streams, and the effects of non-woody and woody litter on metal transfer, accumulation, and storage in streams are poorly understood. Here, we addressed how non-woody and woody litter affect metals in headwater streams in an alpine forest on the Eastern Tibetan Plateau. This area is the source of many rivers and plays an important regulatory role in the regional climate and water conservation. Through comparisons of five metal concentrations, exports and storage in headwater streams with different input conditions of plant litter, our results showed that the input of woody litter could significantly increase flow discharge and increase the metal export ratio in the water. Similarly, the input of non-woody litter could reduce the metal concentration in the water and facilitate the stable storage of metals in the sediment in the headwater streams. Therefore, allochthonous non-woody and woody litter can affect the concentration of metals in water and sediment, and the transfer and accumulation of metals from upstream to downstream in headwater streams. This study provides basic data and new findings for understanding the effects of allochthonous plant litter on the accumulation and storage of metals in headwater forest streams and may provide new ideas for assessing and managing water quality in headwater streams in alpine forests.