Optogenetic-based neuroprosthetic therapies are increasingly being considered for human trials. However, the optoelectronic design of clinical-grade optogenetic-based neuroprosthetic probes still requires some thought. Design constraints include light penetration into the brain, stimulation efficacy, and probe/tissue heating. Optimisation can be achieved through experimental iteration. However, this is costly, time-consuming and ethically problematic. Hence it is highly desirable to have an alternative to excessive animal trials. Thus, a simulation tool for optimising probe design can be an important benefit for the community. The challenge is to understand the interplay between the optical, neural and thermal aspects in the interaction of probe and living neural tissue. In this work, we propose a model which combines these aspects to allow clinically orientated neuroprosthetic teams to design neuroprosthetic probes for optogenetic therapies. Our model provides analyses for optical, thermal and optogenetic electrophysiological processes based on the energy equivalence and exchange among different physical fields. To validate and calibrate the model, optogenetic implantable neuroprosthetic arrayed probes based on miniature LEDs were developed. Then, optical, thermal measurement and neural photocurrent recording experiments were implemented on the probes. We can then provide analysis on exemplar arrayed neural probes.