There are various types of projects you can do. But best way is to perform experiments where you ask a question, construct a hypothesis, test your hypothesis using an experiment and draw conclusions from your experiment.
Parts of a Science Project
1. The Research Question
First you should define your research question (what do you hope to figure out)
2. The Hypothesis
The hypothesis is a possible explanation to your problem.
3. The Procedure
The procedure is the plan for how you will conduct your experiment. In an experiment you change a variable and collect results. You should know the experimental methodolgy and decide on the sample size, what results to be taken etc.
4. The Results
Results are the data, or information, that you collected. Your data should be in numbers.
5. The Conclusion
The conclusion is what you learned from doing the experiment. Your conclusion should explain what happened in your experiment and whether it supported your hypothesis.
What if your results do not support your hypothesis? That is perfectly fine. You're not out to "prove" your hypothesis but to test it.
Presentaion (video) on Science and Engineering Fair projects:
Watch or download the talk on How to conduct a School Science Project presented by Dr Hiran Amarasekera at a Semiar organized by National Science Foundation for Science and Engineering Fair.