What does the black point mean when we are calculate the inductance of several inductors which connected together?
The dots indicate the direction of the magnetic coupling.  In your final circuit, L1 and L2 are coupled so their magnetic fields add, increasing the total inductance; L3, coupled oppositely so the magnetic fields  of L1 and L2 are in opposition to L3 (thereby canceling the magnetic field to some extent), decreases the total inductance.  A similar notation indicates the polarity of a transformer coupling.