A quantum secure multiparty summation protocol is constructed based on the phase shifting operation of d-level quantum system which utilizes the integer-by-integer technique to calculate the modulo d addition. The semi-honest third party prepares d-level two-particle entangled states and transmits the particle sequence composed by all second particles to n secrecy owners. n secrecy owners in turn encode their respective secrecy on this particle sequence through the phase shifting operation. Detailed security analysis turns out that both the outside attack and the participant attack are ineffective towards this protocol. Compared with the quantum secure summation protocols with bit-by-bit calculations, its calculation efficiency is higher; and compared with the protocols with smaller modulo, its applications are more extensive. Especailly, this protocol has extensive applications in the realm of quantum secure multiparty computation, such as quantum multiparty private comparison, quantum multiparty anonymous ranking, quantum multiparty anonymous voting, quantum multiparty key agreement, etc.