In this article we study D1-D3 (or D3) brane systems with generic constant electric and magnetic fluxes in IIB string theory. We work out all possible supersymmetric configurations and find out via T-duality all of them and corresponding supersymmetry conditions could be related to the supersymmetric intersecting D1-D1 pairs. And we do D1-D3 (or D3) open string quantization for a class of configurations. We find that there are many near massless states in NS sector for near-BPS configurations. Furthermore we calculate open string pair creation rate in generic nonsupersymmetric configurations. * Email:bchen01,liuxiaoerty@pku.edu.cn, D-branes and anti-D-branes are nonperturbative objects in string theory, carrying RR charges. A single BPS D-brane preserve half supersymmetries in flat spacetime. But if we put two different D-branes together, or let a D-brane be in a compact configuration, supersymmtry could be broken [1,2]. One typical example is a Dp-anti-Dp system which breaks all the supersymmetries. However, it turns out that when one turns on the background flux on the D-branes, the supersymmetries could be recovered. It is an interesting issue to look for these configurations. In [3], Mateos and Townsend found that if one turned on suitable gauge fluxes on tubular D2-brane, the system can be supersymmetric. This is so-called 'supertube'. The configuration could be taken as the blow-up of D-particles and has no net D2 brane charge. Effectively such system may be simplified to a D2-anti-D2 system with fluxes[4]. This discovery led to a lot of study of supersymmetric Dp-(anti)-Dp system with background fluxes [5,6,7,8]. In particular, it has been found even in Dp-anti-Dp system, the system could be supersymmetric if one turns on suitable fluxes.Another class of non-BPS brane configuration is Dp-Dq with p − p = 0 (mod 4). In particular, D0-D2 system is remarkable. The straightforward calculation of the D0-D2 open string spectrum shows that the ground state is tachyonic, which means that the system is unstable and non-BPS. However, it has been shown in [9] that D0-D2 system is actually dual to the (F1,D1) bound state. In fact, the underlying picture is that through tachyon condensation D0-D2 system settle down to a D0-D2 bound state, with D0 being dissolved into D2. Moreover, if one considers the gauge fluxes on D-brane, the story become more interesting. In D0-D2 system with magnetic field, in the zero-slop limit, there could exist an infinite tower of near massless states in the open string spectrum. On the other hand, the system could be studied in the framework of noncommutative gauge theory. In [10], the authors showed that in D0-D2 system with large magnetic field the D-particle could be taken as the soliton in (2+1)-dimensional noncommutative Yang-Mills theory. The large tower of near massless states corresponds to the fluctuations around the soliton solution. And due to the existence of the large magnetic field, the system is actually near-BPS, and the tachyon condensation could be very well studied, as sho...