The show cause notice was issued to the senior Samajwadi Party leader days after the poll body banned him from campaigning in the state following his controversial 'Kargil' remarks.
He has been asked to respond to the charges by Friday evening, failing which the EC will take a decision without further reference to him.
The EC said it has noted with "deep concern" that despite the ban, Khan "persistently, continuously and wilfully" continued to violate the Model Code of Conduct.
It said the UP minister made provocative statements which can aggravate existing differences and create mutual hatred between communities at Sambhal, Rampur and Bijnor on April nine and ten.
"...the Commission has received further reports/complaints that instead of complying with the EC Order, dated April 11, 2014 in right spirit, you made attempts to circumvent the said directions given in the aforesaid order by making an objectionable remark about ECI during a TV interview...on 13.04.2014 and by getting your objectionable speech read over by one of your party workers, in a recently held election meeting dated April 14, 2014 of Mulayam Singh Yadav," the EC notice said.
It said Khan has made "totally baseless and scurrilous allegations" against the Election Commission.
It noted that prima facie he has violated various provisions of the Model Code of Conduct.
Earlier this month, EC had cracked the whip on Narendra Modi's close aide Amit Shah and Azam Khan by banning them from holding public meetings, processions or roadshows in Uttar Pradesh and asked authorities to initiate criminal proceedings against them.
The EC was also critical of the role of Samajwadi Party's government in the state for "soft-pedalling" on registration of FIRs against Khan and not dealing with the sensitive issue with alacrity.
The EC had later lifted the ban on Shah after he gave a written undertaking that he would not do anything to vitiate the election atmosphere.
Meanwhile, six FIRs have so far been lodged against Khan in various parts of UP following EC's directives.
Khan had triggered a controversy by alleging the 1999 Kargil war was fought and won by Muslim soldiers.
Addressing an election gathering in Ghaziabad recently, Khan had said, "Kargil ki pahadiyon ko fateh karne wale Hindu sainik nahin balki Musalmaan they (Muslim soldiers conquered the hills of Kargil)".