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You have to include your spouse in the application. Whether she is accompanying you or not is your choice.
 
It is mandatory that you include your spouse in your application. You can try listing your spouse as non-accompanying to increase your points. Since your spouse is in Canada with you on a work permit, it's possible CIC may refuse to accept your spouse as non-accompanying since it will be quite obvious that your spouse plans to immediately move to Canada. If you have further questions you should post them in the Express Entry section of the forum.
 
But I include him, my CRS score go down because he has less qualification and no job
You can get up to 20 points from the language skills of your spouse. You can get 6+ points if he has some technical post secondary diploma and 8 points for 3 years bachelor diploma.
You can also get points for qualified Canadian experience of your spouse.
If he is now working in Canada, I would assume, that you can get some language points for starter.
So how about to go for the language evaluation. And yes, student permit or work permit can directly contradict and make the officer doubt the situation.