How to decrease the stepper motor rotate speed as slow as possible?

I am trying to use the tb6560 motor driver (16 micro step) to generate a lowest speed, but it still too fast for me because I need to attach the motor to a flywheel which has a large radius.

You could use a geared stepper motor or a stepper motor with more steps per revolution. You can go to more micro-steps but you might require another controller. More micro-steps gives you higher resolution but also reduces the torque and accuracy.

I always gear to the highest speed required and size the motor torque and steps per resolution to my requirements. If you need more steps you can then go to micro-stepping as a last resort but it may also require increasing the motor size to compensate for the torque loss.

To work out you stepper motor maximum speed to determine the gearing required you can use the spec sheet (how to read a stepper motor spec sheet) and here’s a handy online calculator: