We attempt to develop a possible theory of chemical fractionations in chondrites, that is consistent with various features of chondritic components and current observation of protoplanetary disks (PPD). Combining the 3+2 component fitting calculation that simulates chondrule formation process proposed in paper (I) with additional mixing procedures, we investigate essential causes that made various types of chondrites evolve from the uniform solar system composition, the CI-chondritic composition. Seven chemical types of chondrites (CM, CV, CO, E, LL, L and H) are examined, for which reliable chemical compositions for both bulk chondrites and chondrules therein are known. High vaporization degree of the primordial dust aggregates (dustons) required by the calculation vindicates that the chondrule formation was the driving force for the chemical fractionations in all chondrites examined. Various initial redox states in dustons and different timings of CAIs’ invasion to the chondrule formation zone are identified for different chondrite types. These results, together with a good correlation with the D/H ratios of chondrites measured previously, lead us to the notion that PPD evolved from reducing to oxidizing. We explore the heating mechanism for the chondrule formation and the place it occurred. Only heat source being consistent with our chondrule formation model is lightning discharge. We postulate that large vortices encompassing the snow-line are ideal places for large charge separation to occur between dustons and small ice particles, and that direct strikes on dustons should make them boil for ten seconds and longer and allow a swarm of chondrules released from their surfaces. Chemical fractionations are completed by an aerodynamic separation of dustons from chondrules inside the vortex, in such a way that the dustons fall fast into the vortex center and form a planetesimal immediately, while chondrules with dust mantles fall slow and form a thin veneer on the planetesimal surface. During collisional episodes, the veneers are preferentially fragmented and reassemble themselves by a weak self-gravity to form a rubble-piled chondritic asteroid, i.e. chondrite.