The effect of a bad master's thesis on my future phd Can I do a master's thesis with exploratory work without any results? It's like assume some hypotheses about certain data and testing them. If yes, is that a good thing or a bad thing? Can such a work support me as a good Ph.D. student? 

If I didn't publish anything in my master's level, and I graduated with such a thesis, would that support me or pointing a red flag against my research skills? Add to this, working as a research assistant during my master's studies. Would anyone appreciate my failed attempts and hard work yet not productive? I'm really a hard worker and I'm doing non-traditional approaches (because traditional techniques don't advance/"revolutionize" the field) in my research but I don't have any output. My advisor agrees that we need to do non-traditional approaches to advance our field, but he is pointing out that we need results and to do some baby steps based on a published research. Unfortunately, It's too late now to publish anything. I also feel that this RA job is something against me when I want to apply for a phd program (maybe in a much better school). Would a person who read my application make a statement like this; "2 years as an RA with a good advisor and no a single publication? furthermore a bad thesis? your application is in the trash dear..". I also feel that my advisor feels I'm not really a good RA, and if the time came back, he wouldn't have hired me. Which means that he won't give me a good recommendation letter and most importantly, I let him down. He was very generous to me and provided me a full scholarship and this RA job because he thought I'm really good, but now he thinks the opposite. For me personally, I do believe that I'm not productive, however, I'm learning a lot and I'm a hard worker.

What is the effect of such a situation on me when I want to apply for a Ph.D. program in one of the very good schools (one of the top 200 schools in the world maybe?)
I think the title and body of your post don't exactly match up. 

You can have good research that does not produce results. You can have bad research that does produce results of some kind. You should not base the quality of your research, especially masters level, based on how much of an impact you are making on the field and how revolutionary your results are. A lot of master students don't conduct research and some of them still continue on towards a PhD. Many go straight to a PhD after getting their bachelors- none of them have had any research results. 

I think the bigger issue here is your idea of productivity. There is no way for saying for certain, but it seems like you believe you are unproductive. Why is this the case? It could be founded on a false idea that you need to be constantly publishing (as a masters student) to be "productive" or to get a good recommendation letter. However this is not always the case. 

My recommendation to you is to have a serious talk with your adviser about your thoughts of pursuing a PhD. Ask for advice he might have for you and whether or not he'd recommend you go down that path. You are making a lot of assumptions which are unhealthy- they will only bring your morale further down. PhD environment is much more stressful than a masters environment- my worry for you is that if you are freaking out about research now, it will only get worse in the future. Have a serious conversation with your adviser so you know how you are performing in the eyes of someone else- that should give you the best idea of your chances of getting accepted and then succeeding in a PhD program. Best of luck.