The noun phrase 'new project first meeting today' doesn't work. You can't put five words together in that way and expect them to make sense. The other problem is the lack of articles/determiners. If you say 'I got email' and 'heading to office', it's understandable, but sounds a bit like 'pidgin English'. Here's a suggested rewording. I've rephrased the first sentence to avoid having two 'when' clauses. I was confused by the e-mail I got from my manager when I was heading to the office this morning.
 He told me to call off today's first meeting about the new project. What exactly he is thinking of ?

"call off" = cancel