Pulse transformer reset current simulation in LTspice
Your circuit is flawed. The diode is ineffective. The pulse waveform that drives current into the transformer primary is returning to 0 volts and hence the primary current remains approximately where it got to when the pulse was ramping up the current. This is because: -

$$V = L\dfrac{di}{dt}$$

Hence, if the voltage is zero, then the rate of change of current is zero hence the current doesn't change from where it got to during the active part of the pulse.


  Diode D1 current (Id1 : Red colour ) is in pulsating form as shown in
  the image below.


No, that isn't an effective diode current - it looks like it's probably diode capacitance. The diode does nothing in your circuit.

What you actually need is a switched pulse (that goes open circuit when not pulsing) then, the diode (with a non-zero forward volt drop), will burn off the energy stored in the magnetic field more effectively. Better still, put a resistor in series with the diode to burn energy off at a faster rate.

Or, use a diode and resistor on the secondary to burn off the energy.