This paper investigates the generalized Keller-Segel (KS) system with a nonlocal diffusion term $-\nu(-\Delta)^{\frac{\alpha}{2}}\rho~(1<\alpha<2)$. Firstly, the global existence of weak solutions is proved for the initial density $\rho_0\in L^1\cap L^{\frac{d}{\alpha}}(\mathbb{R}^d)~(d\geq2)$ with $\|\rho_0\|_{\frac {d}{\alpha}} < K$, where $K$ is a universal constant only depending on $d,\alpha,\nu$. Moreover, the conservation of mass holds true and the weak solution satisfies some hyper-contractive and decay estimates in $L^r$ for any $1< r<\infty$. Secondly, for the more general initial data $\rho_0\in L^1\cap L^2(\mathbb{R}^d)$$~(d=2,3)$, the local existence is obtained. Thirdly, for $\rho_0\in L^1\big(\mathbb{R}^d,(1+|x|)dx\big)\cap L^\infty(\mathbb{R}^d)(~d\geq2)$ with $\|\rho_0\|_{\frac{d}{\alpha}} < K$, we prove the uniqueness and stability of weak solutions under Wasserstein metric through the method of associating the KS equation with a self-consistent stochastic process driven by the rotationally invariant $\alpha$-stable Levy process $L_{\alpha}(t)$. Also, we prove the weak solution is $L^\infty$ bounded uniformly in time. Lastly, we consider the $N$-particle interacting system with the Levy process $L_{\alpha}(t)$ and the Newtonian potential aggregation and prove that the expectation of collision time between particles is below a universal constant if the moment $\int_{\mathbb{R}^d}|x|^\gamma\rho_0dx$ for some $1<\gamma<\alpha$ is below a universal constant $K_\gamma$ and $\nu$ is also below a universal constant. Meanwhile, we prove the propagation of chaos as $N\rightarrow\infty$ for the interacting particle system with a cut-off parameter $\varepsilon\sim(\ln N)^{-\frac{1}{d}}$, and show that the mean field limit equation is exactly the generalized KS equation.