Whenever I send mail using SMTP from my website it always goes to SPAM/Junk/Bulk folder of recipient. Is there a way I can make my mails secure so that users may get mails in Inbox and not in SPAM/Junk/Bulk?

The easiest and best way to prevent email from going to a receiver's spam folder is for the user to configure their spam filtering software to allow emeail from you.  This is something the user must do.  On your end, ensuring you're using a legitimate mail server, not a broadband account or an otherwise untrusted source, will help.  Making sure you have the correct DNS and SPF records for your mail server, making sure you allow emails to a postmaster and abuse address and configuring your mail server to stop relaying all help.

Beyond that, send email that doesn't trigger spam filters.  Male enhancement drugs, cheap watches, ladies from overseas and lottery announcements usually get canned.