Feeding a low-protein diet can enhance urea reabsorption and transfer to the rumen, which might alter microbial protein (MCP) synthesis and redirect molecular hydrogen (H2) flow away from methanogenesis. The aim of this study was to determine the effects of feeding goats a low-protein diet on urea nitrogen (N) salvage and metabolism, and consequence on H2 metabolism for MCP synthesis and methanogenesis. Goats (Xiangdong Black goats, a local breed in southern China,) with body weight of 20.4 ± 2.15 kg (mean ± SD) were fed a control diet (consisted of 70% rice straw and 30% concentrates, with crude protein [CP] content by 108 g kg−1) or a low-protein diet (55.2 g CP/kg). 15NH4Cl and 2H2 were employed to further confirm the incorporation of N and hydrogen for MCP synthesis through in vitro culture. Feeding a low-protein diet resulted in greater proportion of retained N (+156%, P < 0.05), plasma urea N (+81.9%, P < 0.05) or rumen ammonia-N (+125%, P < 0.001) relative to digested N and greater renal urea N reabsorption (+11.2%, P < 0.05), together with upregulated relative protein expression of urea transporter A (UTA) in the kidneys (P < 0.05) and mRNA expression of UTA in rumen epithelium (P < 0.05). Feeding low-protein diet resulted in greater concentration of rumen dissolved hydrogen (+55.6%, P < 0.05), ratio of MCP to ammonia-N (+17.6%, P < 0.05), and lower enteric methane emissions (g/kg digested DM, −18.5%, P < 0.05). Further, in vitro experiments verified that the addition of NH4Cl decreased methane and hydrogen production (P < 0.001), although only a minor quantity of headspace 2H2 gas was incorporated for MCP synthesis. In conclusions, feeding a low-protein diet to goats enhances renal urea reabsorption capacity and facilitates the rumen microbial hydrogen incorporation for MCP synthesis, leading to enhanced N retention efficiency and reduced methane emissions. However, the effect of such an approach on livestock performance should be tested in the future studies.