By defining the characteristic length, the boundary effects of Bose-Einstein condensation in a three-dimensional harmonic trap are investigated using the Euler-MacLaurin formula. Results show that the condensed fraction of particles reduces due to the finite-size effects and the effects of finite particle number; the corrections of the condensation fraction and the condensation temperature have, respectively, a maximum value due to the boundary effect, hence it is very effective to optimize the parameters of the harmonic traps for improving the condensation fraction and the condensation temperature. In the jump of heat capacity exist the boundary effects and the effects of finite particle number, and the jump of heat capacity has a minimum because the parameters of harmonic traps are selected to be reasonable. The equation of state is derived for a finite ideal Bose gas system in a three-dimensional harmonic trap; the anisotropy (or isotropy) of the pressure is determined by the anisotropy (or isotropy) of the frequency of the harmonic potential.