Is Science based on Kabbalah?

Science in general is derived from Philosophy. Philosophy is basically the unproven or unanswered questions, and when those questions get answered they get categorized into absolutes, like science and math. Newton may have been trying to show a correlation between the physical world and a heaven and hell, but the theological parts of his studies cannot be put into science, as those questions are still unanswered. The things he could prove and quantify ended up as science.

So to answer your question, science isn't based on the Kabbalah, it is based on a wide array of beliefs that people have proven to be absolute truths. Newton may have been inspired by the Kabbalah, but science has been around for thousands of years. For example, Aristarchus calculated the relative sizes of the Sun, Earth, and Moon about 1400 years before anyone knew about the Kabbalah.

The scientific method was developed and modified over the aeons (and is still debated today!), ever since the first philosopher ever pondered existential questions (questions about existence/reality) and tried to understand various natural phenomena reasonably – not by using linguistic trickery or ad-hoc supernatural explanations.