This paper presents observations of a protoplanetary disk around the Herbig Ae star HD 163296 in (CO)-C-12 (J = 1-0), (CO)-C-12 (J = 3-2), (CO)-C-13 (J = 1-0), and (CO)-C-13 (J = 3-2) emission lines. Double-peaked emission profiles originating from the rotating circumstellar disk were detected in all of the lines. The disk parameters were estimated from model calculations in which the radial distribution of the temperature or surface density inside the disk had a power-law form. The surface density should be sufficiently high so that the disk is optically thick for all of the CO lines, as discussed in previous studies based on interferometric observations. The temperature and outer radius of the disk were also confirmed to be consistent with the previous results. Taking advantage of the difference in the position of the photosphere among the CO lines, we revealed the temperature distribution in the vertical direction. The temperature of the (CO)-C-12 (J = 3-2) emitting region is about twice higher than that of any other CO emitting region; the former is 58.5 +/- 9.5 K, while the latter is 31 +/- 15K at 100 AU from the central star, suggesting that there are at least two distinct temperature regions. The best-fit temperature for (CO)-C-13 (J = 1-0) that should trace the deepest region of the disk is even lower, implying that there is also a different temperature region deep inside of the disk. Such a vertical temperature distribution in a disk was identified both in T Tauri and Herbig Ae stars (e.g., DM Tau, AB Aur, and HD 31648), and this should be a common feature in protoplanetary disks.