He also said that he has not decided on his future plans yet.
"A party should have certain principles. Sometimes Trinamool Congress is with the BJP, sometimes they are with the Congress. They sometime term the BJP as communal, sometime say they are not communal," Roy told the media at his residence here.
"We were very much a part of the NDA government once and joined hands with the BJP. Now the party thinks that the country cannot go ahead without the Congress.
"These things compelled me to leave the party with a heavy heart," he said shortly after submitting his resignation to Vice President M. Venkaiah Naidu, who is also the Chairman of the upper house.
Claiming that the Trinamool was formed to fight against the policies of Congress and had been their biggest political rivals for a long time, Roy said the two parties should merge if Trinamool leadership now considers Congress to be imperative for the country's progress.
"From 2012 to 2014, Trinamool Congress was the main opposition of the Indian National Congress in national politics and inside and outside the floor of parliament. During that time, it strongly opposed Congress on issues of 2G spectrum, coal and the Commonwealth Games scam.
"But again after 2014, Trinamool feels that without Congress, the country cannot run. We have formed a political party to fight against the Congress. If we feel that without Congress the country cannot go ahead, let us move for the merger of the parties. Why the different parties would be kept?" he asked.
Stating that "dynasty politics is there all over India", Roy hinted at presence of such practices in the Trinamool and that it could also be the reason behind his exit.
Revealing that he was in touch with the senior leadership of all the parties, Roy said he would take a decision about his future endeavours after Diwali.
"I have not taken any decisions about the future plans yet. I would go for a leave now. I will decide whether I would join any political parties or float a new party after the Kali Puja (Diwali)," he added.
In a veiled attack at party supremo Mamata Banerjee, Roy said "one man parties" like the Trinamool are not good for the country and claimed everyone in the party should be treated as comrades and not as servants of an individual.
"Nationalised parties are needed for country's betterment. Since the inception of the party we have considered Mamata Banerjee as the leader. But I think we all are comrades of a party not servant of an individual," said Roy, once Banerjee's right hand man.
"I am not saying that all the party workers are servants but the manner in which the party is being run by one person, it is as good as that," he said.
He also revealed that the speculations about Trinamool's connection with the Rashtriya Swayamsevak Sangh in the state are true and said then Vishwa Hindu Parishad leader Ashok Singhal had come to meet Banerjee.
"In 2003 we made contact with the RSS people as directed by the party (Trinamool Congress). It is true that Ashok Singhal came to meet Mamata Banerjee. It is also true that I had a connection with the RSS and BJP," he added.