In a letter to Victorian Liberal Party president Greg Mirabella seen by AAP, Senator Van said he could not remain a member of a party that "tramples upon the very premise on which our justice system is predicated".
It follows uproar over bombshell allegations against the senator by Independent senator Lidia Thorpe and former Liberal senator Amanda Stoker this week.
They both alleged Senator Van touched them inappropriately in previous years, which he has denied.
On Friday, Opposition Leader Peter Dutton confirmed further allegations have been brought against Senator Van and called on him to quit parliament.
"Given the Liberal Party's wholesale disregard for due process and natural justice in relation to allegations made against me, I write to resign my membership effective immediately," Senator Van wrote in the resignation letter.
"I cannot remain a member of a party that tramples upon the very premise on which our justice system is predicated.
"This is a travesty of justice and I reiterate that I deny the allegations made against me.
"I resign also acknowledging the cruel irony of doing so amidst public discourse about the weaponisation of allegations and the role of the rule of law which has at its centre the presumption of innocence."
Senator Van said he was "deeply distressed and hurt" and had been denied "procedural fairness".
"I acknowledge the hundreds of members, friends and my family, who have shown me support in my final days as a member," he said.
"I am grateful for their belief in my honesty and integrity.
"I have worked tirelessly for the party and fought hard for its beliefs over many years."
Senator Van said he would continue to fight for "what I thought were the party's values - just not under its banner".
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