TSUBAME2 consists of more than 1400 compute nodes interconnected by high-bandwidth full bisection-bandwidth Infiniband networks. There are three node types: Thin, Medium, and Fat nodes, which differ in their equipped memory capacity among others. All compute nodes share scalable storage systems that provide 7PB of capacity.

| Node Name | Purpose | # | Node Product Name | CPU | GPU | Memory | Local Storage (SSD) | Network |
| Thin Node | For jobs needing less than 54GB | 1408 | HP Proliant SL390s G7 | Intel Xeon 2.93 GHz (6 cores) x 2 (Hyperthreading enabled) | NVIDIA Tesla M2050 x 3 | 54GB (partly 96GB) | 120GB (partly 240GB) | QDR InfiniBand x 2 (80Gbps) |
| Medium Node | For jobs requiring up to 128GB | 24 | HP Proliant DL580 G7 | Intel Xeon 2.0 GHz (8 cores) x 4 (Hyperthreading enabled) | NVIDIA Tesla S1070 | 128GB | 480GB | QDR InfiniBand x 1 (40Gbps) |
| Fat Node | For jobs using more than 128GB and up to 256/512GB | 10 | HP Proliant DL580 G7 | Intel Xeon 2.0 GHz (8 cores) x 4 (Hyperthreading enabled) | NVIDIA Tesla S1070 | 256GB/512GB | 480GB | QDR InfiniBand x 1 (40Gbps) |