We demonstrate compact transmission soft X-ray microscope system with 50 nm spatial resolution for the life and physical science. This x-ray microscope operates at photon energy from 284 eV to 543 eV, so called 'water window' region (2.3~4.4nm), where natural contrast between carbon (protein) and oxygen(water) allows imaging of unstained biological material in their natural, hydrated environment. The compact transmission soft x-ray microscope is based on a laser plasma x-ray source, tandem ellipsoidal condenser reflective optics, diffractive zone plate optics and x-ray sensitive charge-coupled device (CCD) to record an x-ray image. The source is a liquid-jet target laser plasma source, which is practically debris free and suitable for high average power operation. The flux, brightness and bandwidth of this source has been simulated and optimized for X-ray microscopy for biology application. A tandem ellipsoidal reflective mirror operates as condenser and illuminates the sample. The high resolution imaging is currently performed with a ~12% efficient nickel zone plate with an outmost zone width of 35nm. In conclusion, we suggested a possibility of the compact soft x-ray microscopy system with 50 nm spatial resolution as a suitable tool for the wide range of studies such as biological imaging, environmental samples, and nanostructure analysis.