9. B.

Since the least common multiple of $2,3,5$ is 30, and the number of small rectangular prisms with edge lengths of $2,3,5$ that a diagonal of a cube with edge length 30 passes through is $\left[\frac{30}{2}\right]+\left[\frac{30}{3}\right]+\left[\frac{30}{5}\right]-\left[\frac{30}{2 \times 3}\right]-\left[\frac{30}{2 \times 5}\right]-\left[\frac{30}{3 \times 5}\right]+\left[\frac{30}{2 \times 3 \times 5}\right]=22$, therefore, the number of small rectangular prisms that a diagonal of a cube with edge length 90 passes through should be $3 \times 22=66$.