This work reports both numerical and experimental studies of the reconditioning of a microwave plasma jet chemical vapor deposition (MPJCVD) system for the growth of diamond film. A three-dimensional plasma fluid model is constructed for investigating and conditioning the MPJCVD system and optimizing its operating conditions. The methodology solves electromagnetic wave and plasma dynamics self-consistently using an adaptive finite element method as implemented in COMSOL Multiphysics. The whole system has been modeled under varying parameters, including the reactor geometry, microwave power, and working gas pressure. Using an operating condition identical to the optimized simulation results, the MPJCVD system successfully fabricates a diamond-thin film on a graphite substrate. The SEM image reveals the presence of a diamond film uniformly distributed with particles of a size of ~1 μm. The field emission from the diamond film grown from our homemade MPJCVD system on the graphite substrate presents extraordinary properties, i.e., extremely high current density and relatively low turn-on voltage. The turn-on electric field observed could be as low as ~4 V/μm. This developed model provides valuable physical insights into the MPJCVD system, which guided performance improvements. The work may find applications in surface hardening and provide a better cold cathode for field electron emission.