Under ergodic condition, the analytic expressions for the fluctuations of temperature and particle number in the well of a system are obtained rigorously in particle-spilling-from-well model by means of integration approaches in phase space; the relationships among fluctuations of thermodynamic variables, the total particle numbers, and the well volume are emphasized. Results show that the less the total number of particles and the smaller the well's volume, the more remarkable the thermodynamic fluctuations effect, and the more closely the thermodynamic fluctuations related to the particle spilling from the well. There is a one to one correspondence between particle spilling from the well and the occurrence of negative specific heat, and the huge thermodynamic fluctuations,as well as, the origin of this phenomenon can be understood by the apparent energy inverse partition.