I got my immigration petition for alien worker denied. Will it effect my H-1 petition?

No. They are two different petitions and should not effect each other. Unless of-course I-140 was revoked due to fraud.

Depends on the reasons for the denial. On an eligibility denial, probably not. Denial based on misrepresentation, yes.

H-1B is a dual intent status, and having prior immigrant intent will not cause an H-1B denial.

The denial of the FORM I-140 filed on your behalf will not impede a petition for the H-1B. However. non-immigrant visas that are not dual intent are now out of reach.

You should be concerned because the H-1B requires non-immigrant intent & because your employer filed the I-140 which is a petition for permanent residence. However, I have a few questions why was the I-140 denied? The Labor Certification Application that must be filed with the US Department of Labor (DOL) before the I-140 is filed is much harder in my opinion than the I-140. If the Labor Certification Application is certified by the DOL the I-140 is usually approved unless the applicant is inadmissible for some other reason. Also the H-1B applications are used up on the 1st day they become available and I believe that no more H-1B petitions will be available until April of 2016.