How to upload a big CSV file in SAP Hybrid mobile app quickly?

As you said you are using the hot folder concept, you need to ensure that the proper threads are being used at every moment for any operation.

By default, the number of threads used for import is one. To be more technical, impex.import.workers thread is one if not set explicitly. Since in your case the file is big, make sure that you exploit all the available cores to the fullest. It is highly recommended that maximum threads at any point of time should not be more than twice the number of cores. For optimal working, you may need to work out test again and again till you get the work done with acceptable limit.