Assalamualaikum If we consider smoking as khamr then does the hadeeth of prayer not accepted for 40 days applies to a smoker too. There is also the hadeeth of a person who drinks wine and then repents 3 times after which,if he drinks again, Allah won't accept his repentance.So this hadeeth also applies to a person who consumes khamr(smokes cigarette)i.e repentance of a smoker who repented from smoking one hundred times will not accepted?

All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. 

There is no doubt that smoking cigarettes is harmful, but it is different from alcohol as it does not affect the mind as alcohol affects the mind. For more benefit, please refer to Fataawa 81589 and 81345.

Secondly, the prohibition of smoking cigarettes is taken from general indications of the prohibition of evil and wasting money and the harm that it causes. However, there are specific passages from the Quran and Sunnah texts regarding the prohibition of alcohol, so it is not correct to say, as you mentioned, that the Hadd (the prescribed punishment in the Islamic Law) for drinking alcohol should be applied to a cigarette smoker as well.

In addition, the acceptance or non-acceptance of the prayers of a cigarette smoker for forty days is a matter of the unseen that cannot be known except through revelation. Therefore, this cannot be based on personal opinion or analogy to drinking alcohol.

In short, smoking cigarettes is forbidden but not to the same degree as drinking alcohol, and if a cigarette smoker knows that it is prohibited, he may be punished in a way that may deter him from smoking. Shaykh Ibn ‘Uthaymeen said in Ash-Sharh Al-Mumti’: “If we see someone smoking cigarettes and he believes that it is lawful, then we do not discipline him with a discretionary punishment (T'azeer); and if he believes that it is forbidden then we discipline him, because Ta'zeer is an obligation for every sin that has no specific Hadd or expiation.” [End of quote]

As regards what you mentioned that Allaah does not accept the repentance of a drinker of alcohol, then this needs explanation. The Hadeeth which reads: “Whoever drinks alcohol even if it is one sip, his repentance will not be accepted for forty days; but if he repents, Allaah will accept his repentance. If he drinks again, his repentance will not be accepted for forty days, and if he repents, Allaah will accept his repentance. If he does that again, then Allaah will give him the fluid flowing from the inhabitants of Hell to drink on the Day of Judgment.” [An-Nasaa’i, Ibn Maajah, and At-Tirmithi] The narration of At-Tirmithi reads: “If he does that again the fourth time, Allaah will not accept his prayers for forty days, and if he repents, Allaah will not accept his repentance and He will give him to drink from the river of the fluid flowing from the inhabitants of Hell.”

In the Hadeeth, it says that Allaah accepts his repentance the first times, and Allaah not accepting his repentance the last time means either that the sinner will not be favored with repentance, or that this is said as an emphasis on deterrence. As-Sindi, said in his commentary on Sunan Ibn Maajah: “Apparently, his repentance will not be accepted this time. This is explicitly mentioned in another Hadeeth. This is problematic, unless the Hadeeth means that he will not be favored with repentance this time.” [End of quote]

Tuhfatul-Ahwathi reads: (...if he repents, then Allaah will not accept his repentance...) This is an emphasized warning and severe deterrence. On the other hand, another Hadeeth states: “The one who asks for forgiveness is not one who insists (on sinning) even if he returns to the sin seventy times in a day.” [narrated by Abu Bakr As-Siddeeq and reported by Abu Daawood and At-Tirmithi]

Allaah Knows best.