Transition metal selenides nanoparticles/carbon composites have been one of the promising lithium/sodium ion battery anodes. In the present study, NiSex nanoparticles encapsulated into microporous flowerlike carbon have been prepared by a hydrothermal route directed by the flowerlike Ni/C composite template. In a low hydrothermal temperature (i.e., 120 degrees C), the metallic Ni nanoparticles are transformed into Ni0.85Se, which has an average particle size of similar to 13.02 nm. The selenization degree and particle size can be obviously improved at a higher hydrothermal temperature (i.e., 160 or 180 degrees C), accompanying with the decrease in carbon content, and partial Ni0.85Se nanoparticles have been transformed into NiSe2. As anode of lithium ion batteries, the NiSex obtained at 180 degrees C (i.e., 180 degrees C-NiSe) can deliver a higher discharge capacity (e.g., 851.0 mA h g(-1) after 100 cycles at 0.2 A g(-1)) and better cycling stability compared with the low temperature obtained sample. However, the rate capability and sodium ion storage performance of 120 degrees C-Ni0.85Se are better than the 180 degrees C-NiSex, and a discharge capacity of 326.5 mA h g(-1) can be reached at a high rate of 5 A g(-1) for 120 degrees C-Ni0.85Se. Also, a high capacity retention ratio of 64.3% after 100 cycles can be reached for 120 degrees C-Ni0.85Se as sodium ion battery anode. The different electrochemical performance can be attributed to the decreased particle size.