For the traditional metal heaters used for SOI (silicon-on-insulator)-nanowire de- vices, a thick SiO2 upper-cladding layer is usually needed between the metal heater and the silicon core to isolate metal absorption, which makes the thermal tuning be with low response speed, low heating efficiency, and low maximal temperature. In this paper, we propose and demonstrate a graphene-based transparent nano-heater for SOI nanowires. The present transparent graphene nano-heater is designed to contact directly with the silicon core of an SOI nanowire by utilizing the transparency of graphene. The lack of the thick SiO2 upper-cladding layer between the heater and the core region helps make fast thermally-tuning nanophotonic integrated devices. It is also beneficial to improve the heating efficiency because the heating volume is shrunk significantly. The graphene nano-heater is designed optimally to avoid any significant excess loss for the guided modes in the SOI nanowires. For example, the theoretical propagation losses of T E- and T M - polarization modes of a 600 nm-wide SOI nanowire with a 100 nm-wide graphene nano-heater are as low as ∼ 0.005 dB/µm and ∼ 0.013 dB/µm respectively. With this graphene-based trans- parent nano-heater, we present a thermally-tuning silicon Mach-Zehnder interferometer (MZI). The power consumption to have π phase-shift is ∼ 5.2 mW and ∼ 5.7 mW for T E- and T M - polarization modes, respectively. The theoretical response time is ∼ 4.4 µs, which is about twice faster than that for the case of using a traditional metal heater. In addition, the temperature of the silicon core is almost the same as that of graphene nano-heaters. In contrast, for the case of traditional metal heaters, the silicon core has much lower temperature than the metal heater while the metal heater has a limited maximal operation-temperature. This indicates that one can achieve higher achievable temperature for the silicon core with the present graphene nano- heater than the traditional metal heater. Graphene can also be used as a heat conductor (other than heater) by utilizing its high thermal conductivity of up to 5300 W/mK. The excellent ther- mal properties of graphene make it very useful to enable efficient thermally-tuning nanophotonic integrated devices including optical switches, optical filters, etc..