You can find the answer in this link http://www.chinabtp.com/android-pdf-viewer-library-or-mupdf-library-tutorials/
Here is the instruction:
Building a MuPDF lib on windows with Cygwin and android-ndk
Download MuPDF 1.3 Source from https://code.google.com/p/mupdf/downloads/list unzip to folder c:/mupdf-1.3-source
Install Cygwin: Download and run Run setup-x86.exe from http://cygwin.com/install.html when installing cygwin, make sure you selected make packages and C++ compilers
Make generate. open cygwin terminal, run
cd /cygdrive/
cd c/mupdf-1.3-source
make generate
Install android-ndk: download android-ndk-r9d-windows-x86.zip and unzip it to
c:/android-ndk-r9d
Build mupdf lib: on windows cmd console:
preparation:
cd c:/mupdf-1.3-source/platform/android
copy local.properties.sample local.properties
edit local.properties, uncomment
#sdk.dir=C:\\Program Files (x86)\\Android\\android-sdk
and change to
sdk.dir=REAL andforid-sdk Folder
build: while still on c:/mupdf-1.3-source/platform/android, run:
/android-ndk-r9d/ndk-build
Upon the completion of the build, a folder named libs will be created under
c:/mupdf-1.3-source/platform/android
Create android apk. Open eclipse, create a new android project from existing code, browse to c:/mupdf-1.3-source/platform/android, now you can create a mupdf apk.