您可以在切片上使用numpy.random.shuffle（shuffle作用于第一个轴，这是您想要的）：

# shuffle in place
np.random.shuffle(a[:, [0,2,3]])

# see changes
print(a)

输出：

[[1 3 9 8 4]
 [2 4 6 1 9]
 [7 3 0 5 8]
 [1 6 9 2 4]]

要使用的完整代码：

column_indices = [0,2,3]

a = np.array([[1,3,9,8,4],
              [2,4,6,1,9],
              [7,3,0,5,8],
              [1,6,9,2,4]])

# transpose to switch from columns to rows
shuffled = a[:, column_indices].transpose()
np.random.shuffle(shuffled)

a[:, column_indices] = shuffled.transpose()
a