Various spatial analysis problems exist in many scientific fields such as geology

geophysics

oceanography

agriculture

ecology

environmental science

geography

sociology

politics

anthropology among others. So far

commercial GIS software provided only very simple analytic functions of overlay and classic statistics

which are far from being sufficient. However

many spatial analysis software packages were developed independently. Compared to the 500-years development history of modern mathematics

the mathematical theoretic foundations of spatial analysis have been developed for just 20～30 years. It is still in very preliminary stage and far from being mature.In this paper

after a brief review of the spatial analysis functions in existing GIS software and the need of spatial analysis functions of geoscience

a comparative study was conducted between two typical spatial analysis packages. Based on these

the further development of spatial analysis functions is explored in both contents and strategies. We conclude that for a short-term objective

the existing spatial analysis packages can be integrated with the GIS in different level based on the practical need. However

for a long-term consideration

a mathematical framework of spatial analysis needs to be developed.